From pankaj at nii.res.in Sun Feb 1 08:02:11 2004 From: pankaj at nii.res.in (Pankaj) Date: Sun, 01 Feb 2004 18:32:11 +0530 (IST) Subject: [BiO BB] (no subject) Message-ID: hi all, i have a set of sequences whose similarity among themselves is very poor. i want to have a good threading program which can thread these sequences on a known structure (as i know that all of them take the same fold). i have read somewhere that threading programs can thread any sequence onto any strcuture...in that case how do i make sure that the threading result is right? please suggest me some good threading programs which can be downloaded and run locally on the computer. thanks in advance pankaj From idoerg at burnham.org Sun Feb 1 10:24:42 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Sun, 1 Feb 2004 07:24:42 -0800 Subject: [BiO BB] (no subject) In-Reply-To: Message-ID: Hi Pankaj, Threaders can predict folds for a larger chunk of sequences than, say, homology modelling, but they cannot place "any sequence onto any structure" because: 1) We do not know all the strucutres. 2) The energy functions are not 100% specific and sensitive. Errors do occur. I guess what you would really like is a good strucutre prediction program. I would start with a web-based metaserver. The metaservers incorporate information form different structure prediction programs, and thus sometimes achieve better results than one specific program. You can then look into the results of the individual programs, decide what you like, and in many cases download it for standalone running. One such metaserver is: http://bioinfo.pl/Meta/ The quality of the individual servders is evaluated here: http://bioinfo.pl/LiveBench/ With links to the server sites. I hope this helped, Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo On Sun, 1 Feb 2004, Pankaj wrote: > hi all, > i have a set of sequences whose similarity among themselves is very > poor. i want to have a good threading program which can thread these > sequences on a known structure (as i know that all of them take the > same fold). > i have read somewhere that threading programs can thread any sequence > onto any strcuture...in that case how do i make sure that the > threading result is right? > please suggest me some good threading programs which can be downloaded > and run locally on the computer. > thanks in advance > pankaj > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From Austin.Tanney at arragen.com Mon Feb 2 04:22:04 2004 From: Austin.Tanney at arragen.com (Austin Tanney) Date: Mon, 2 Feb 2004 09:22:04 -0000 Subject: [BiO BB] Please guide me Message-ID: I have to say I am very much with Dan on this one. Java and Perl work for bioinformatics applications. If someone is going to learn a programming language, why not learn one that will be more generally applicable. Bioperl and Biojava have already made a lot of headway into creating a lot of shortcuts for bioinformatics applications anyway. If a specific language was developed purely for bioinformatics, people would still need to learn that language.. if you are going to take the time to learn a language why not learn one that you can use for more than just bioinformatics? Austin > it may be pluggable, but i don't want to speculate. i just have an idea for a > future. in short > we can build language for JVM for example which uses all what Java ( notice 3d > here too) can provide but completely hiddens it from > bioinformatics programmer. i'm sure i'll find problems with existing solutions > (bioperl and biojava) when i put my hands on it. and yes, ease of use is a main > reason for such custom language. and i guess it means how language is presented > for a researcher. i doubt > plain java is applicable. sounds like the tower of babel gone wrong - java, perl, c, all are good for bioinformatics, laying the concepts on top is the tricky part, and the more you ask a language to do for you, the more 'locked in' to a particular mind set you get. Traditional programing languages are good because of the freedom of they give - beyond that it is a matter of taste. I do not think each dicipline of science should have its own language. subroutines yes, dialect no. This e-mail is from ArraGen Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk at arragen.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraGen Ltd. Registration Number NI 43067 Registered Address : Almac House, Charlestown Road, Craigavon, BT63 5UA Northern Ireland From dmb at mrc-dunn.cam.ac.uk Mon Feb 2 07:43:09 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 2 Feb 2004 12:43:09 -0000 (GMT) Subject: [BiO BB] Please guide me In-Reply-To: References: Message-ID: <46070.193.60.81.207.1075725789.squirrel@www.mrc-dunn.cam.ac.uk> ++ Austin Tanney-- > I have to say I am very much with Dan on this one. Java and Perl work for > bioinformatics applications. If someone is going to learn a programming language, > why not learn one that will be more generally applicable. Bioperl and Biojava have > already made a lot of headway into creating a lot of shortcuts for bioinformatics > applications anyway. If a specific language was developed purely for > bioinformatics, people would still need to learn that language.. if you are going > to take the time to learn a language why not learn one that you can use for more > than just bioinformatics? > > Austin Although having said that, some friends of mine are working on a bioinformatics language! > >> it may be pluggable, but i don't want to speculate. i just have an idea for a >> future. in short >> we can build language for JVM for example which uses all what Java ( notice 3d >> here too) can provide but completely hiddens it from >> bioinformatics programmer. i'm sure i'll find problems with existing solutions >> (bioperl and biojava) when i put my hands on it. and yes, ease of use is a main >> reason for such custom language. and i guess it means how language is presented >> for a researcher. i doubt >> plain java is applicable. > > sounds like the tower of babel gone wrong - java, perl, c, all are good for > bioinformatics, laying the concepts on top is the tricky part, and the more you > ask a language to do for you, the more 'locked in' to a particular mind set you > get. Traditional programing languages are good because of the freedom of they give > - beyond that it is a matter of taste. I do not think each dicipline of science > should have its own language. subroutines yes, dialect no. > > > > > > This e-mail is from ArraGen Ltd > > The e-mail and any files transmitted with it are confidential and privileged and > intended solely for the use of the individual or entity to whom they are > addressed. > > Any unauthorised direct or indirect dissemination, distribution or copying of this > message and any attachments is strictly prohibited. > > If you have received the e-mail in error please notify helpdesk at arragen.com or > telephone +44 28 38 363841 and delete the e-mail from your system. > > E-mail and other communications sent to this company may be reviewed or read by > persons other than the intended recipient. > > Viruses : although we have taken steps to ensure that this e-mail and any > attachments are free from any virus, you should, in keeping with good practice, > ensure that they are actually virus free. > > ArraGen Ltd. Registration Number NI 43067 > Registered Address : Almac House, Charlestown Road, Craigavon, BT63 5UA Northern > Ireland > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From landman at scalableinformatics.com Tue Feb 3 01:13:02 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Tue, 03 Feb 2004 01:13:02 -0500 Subject: [BiO BB] updated NCBI RPMs following the release of new NCBI code Message-ID: <1075788782.26179.39.camel@protein.scalableinformatics.com> Hi folks: We built RPMs of the newly released NCBI code. You can pull them from here: http://downloads.scalableinformatics.com/downloads/ncbi/ . These include a patch to enable the RPM to build on a SUSE SLES 8.x based Opteron system. We do not have a Redhat x86_64 system to test the build on, so we cannot verify that platform either. The patch we created to complete the x86_64 support can be found at http://downloads.scalableinformatics.com/downloads/opteron/ncbi/opteron-m64.patch . This time around, we included simple optimization patches to the linux*.ncbi.mk files, and built specific versions for athlon and opteron. A Pentium 4 patch is there as well, though we cannot test that easily (no .p4.rpm target, and we need i686 to be able to run across P3 and higher architectures). Suggestions for what to do here are welcome. As usual, bug reports back to me, and we will try to get fixes out quickly. Joe -- Joseph Landman, Ph.D Scalable Informatics LLC email: landman at scalableinformatics.com web: http://scalableinformatics.com phone: +1 734 612 4615 From dirimarslan at superonline.com Wed Feb 4 07:24:11 2004 From: dirimarslan at superonline.com (Dirim Arslan) Date: Wed, 4 Feb 2004 14:24:11 +0200 Subject: [BiO BB] Questions about gene discovery? In-Reply-To: <20040203170108.DDB7ED1F16@www.bioinformatics.org> Message-ID: <20040204121954.47D31D1F0C@www.bioinformatics.org> Hi, I am a molecular biology student. I've some questions based on computional biology, I have a 723bp long nucleic acid sequance, i have to find this sequance's physical map, orthologues's, phylogenetic pattern. How can i find these features of my gene? What is the most populer searching tool for each one? Thanks alot! Dirim From landman at scalableinformatics.com Wed Feb 4 10:54:04 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 04 Feb 2004 10:54:04 -0500 Subject: [BiO BB] FYI: BLAST 2.2.7 - tblastx BUG Message-ID: <1075910044.3935.29.camel@protein.scalableinformatics.com> I will update the RPM's on http://downloads.scalableinformatics.com as soon as the new code is available. -----Forwarded Message----- Subject: [blast-announce] [ BLAST-Announce #039]: BLAST 2.2.7 - tblastx BUG Date: Wed, 04 Feb 2004 10:45:31 -0500 BLAST 2.2.7 contains a flaw which results in incorrect tblastx alignments. The flaw ONLY affects tblastx. A fix will be available shortly. We will make an announcement through blast-announce and on the web pages when this is available. We are improving our automatic quality assurance process to better detect such errors in the future. Sincere apologies for the inconvenience. The BLAST team From dirim at kablonet.com.tr Wed Feb 4 07:14:44 2004 From: dirim at kablonet.com.tr (Dirim Arslan) Date: Wed, 4 Feb 2004 14:14:44 +0200 Subject: [BiO BB] Questions about gene discovery? In-Reply-To: <20040203170108.DDB7ED1F16@www.bioinformatics.org> Message-ID: <20040204121100.8F2BCD1F0D@www.bioinformatics.org> Hi, I am a molecular biology student. I've some questions based on computional biology, I have a 723bp long nucleic acid sequance, i have to find this sequance's physical map, orthologues's, phylogenetic pattern. How can i find these features of my gene? What is the most populer searching tool for each one? Thanks alot! Dirim From rajat at isical.ac.in Thu Feb 5 00:16:13 2004 From: rajat at isical.ac.in (Rajat Kumar De) Date: Thu, 05 Feb 2004 10:46:13 +0530 Subject: [BiO BB] request for suggestion Message-ID: <4021D19C.5CE9295F@isical.ac.in> Dear Colleague, I am looking for some papers on the mathematical modeling of following controlling factors of gene expression. It would be a great help to me, if somebody can provide me some papers/links or some suggestions, on the mathematical models of these factors in controlling gene expression. The controlling factors are: 1. Chromatin Structure 2. Transcriptional Initiation 3. Transcript Processing and Modification 4. RNA Transport 5. Transcript Stability 6. Translational Initiation 7. Post-Translational Modification 8. Protein Transport 9. Control of Protein Stability Please also let me know, if there are other controlling factors of gene expression. Regards, Rajat ****************************************************************** * Rajat K. De, Ph.D. | Telephone * * Assistant Professor | Office : 91-33-25753105 * * Machine Intelligence Unit | Residence : 91-33-25796860 * * Indian Statistical Institute | Mobile : 91-9830013571 * * 203 B.T. Road | Fax : 91-33-25783357 * * Kolkata 700108 | 91-33-25773035 * * INDIA. | Email : rajat at isical.ac.in * ****************************************************************** From j.d.tucker at vla.defra.gsi.gov.uk Thu Feb 5 09:29:36 2004 From: j.d.tucker at vla.defra.gsi.gov.uk (Tucker, James) Date: Thu, 5 Feb 2004 14:29:36 -0000 Subject: [BiO BB] (no subject) Message-ID: <104FE795DA19D411A71A0008C733F76404A43BCB@vla6> Hi all, I'm looking for software that will indicate if I have a secretion protein or not. I'm also looking for some software that will find cleavage site within my seq. Any suggestions ?? Regards James James Tucker Brucella Research Group Department of Bacterial Diseases VLA Weybridge Woodham Lane New Haw Addlestone Surrey KT15 3NB Tel: ++44(0)1932 357227 / 359595 Fax: ++44(0)1932 357873 mailto:j.d.tucker at vla.defra.gsi.gov.uk Veterinary Laboratories Agency (VLA) This email and any attachments is intended for the named recipient only. Its unauthorised use, disclosure, storage or copying is not permitted. If you have received it in error, please destroy all copies and inform the sender. Whilst this email and associated attachments will have been checked for known viruses whilst within VLA systems we can accept no responsibility once it has left our systems. Communications on VLA's computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes. From pajailwala at yahoo.com Thu Feb 5 10:08:27 2004 From: pajailwala at yahoo.com (Parthav Jailwala) Date: Thu, 5 Feb 2004 07:08:27 -0800 (PST) Subject: [BiO BB] request for suggestion In-Reply-To: <4021D19C.5CE9295F@isical.ac.in> Message-ID: <20040205150827.76478.qmail@web12304.mail.yahoo.com> Dear Mr. Rajat, You have considered most of the factors here, however, I am not sure if you have also included 'Alternative splicing' in one or more factors listed below. Alternatively spliced forms of the same protein would indirectly affect transcript stability and/or protein transport. so it looks important to me. Parthav Jailwala Rajat Kumar De wrote: Dear Colleague, I am looking for some papers on the mathematical modeling of following controlling factors of gene expression. It would be a great help to me, if somebody can provide me some papers/links or some suggestions, on the mathematical models of these factors in controlling gene expression. The controlling factors are: 1. Chromatin Structure 2. Transcriptional Initiation 3. Transcript Processing and Modification 4. RNA Transport 5. Transcript Stability 6. Translational Initiation 7. Post-Translational Modification 8. Protein Transport 9. Control of Protein Stability Please also let me know, if there are other controlling factors of gene expression. Regards, Rajat ****************************************************************** * Rajat K. De, Ph.D. | Telephone * * Assistant Professor | Office : 91-33-25753105 * * Machine Intelligence Unit | Residence : 91-33-25796860 * * Indian Statistical Institute | Mobile : 91-9830013571 * * 203 B.T. Road | Fax : 91-33-25783357 * * Kolkata 700108 | 91-33-25773035 * * INDIA. | Email : rajat at isical.ac.in * ****************************************************************** _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Do you Yahoo!? Yahoo! Finance: Get your refund fast by filing online -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgollery at unr.edu Thu Feb 5 13:05:26 2004 From: mgollery at unr.edu (Martin Gollery) Date: Thu, 5 Feb 2004 10:05:26 -0800 Subject: [BiO BB] (no subject) In-Reply-To: <104FE795DA19D411A71A0008C733F76404A43BCB@vla6> References: <104FE795DA19D411A71A0008C733F76404A43BCB@vla6> Message-ID: <1076004326.402285e607b4c@webmail.unr.edu> Hi James, Take a look at TargetP. The website is http://www.cbs.dtu.dk/services/TargetP/ One of the nice things about this site is that it allows you to analyze many sequences at once- I ran 140 proteins yesterday. Much nicer than those sites that require one at a time cut and pasting! Cheers, Marty Quoting "Tucker, James" : > > Hi all, > I'm looking for software that will indicate if I have a secretion protein > or > not. > I'm also looking for some software that will find cleavage site within my > seq. > Any suggestions ?? > Regards > James > James Tucker > Brucella Research Group > Department of Bacterial Diseases > VLA Weybridge > Woodham Lane > New Haw > Addlestone > Surrey > KT15 3NB > > Tel: ++44(0)1932 357227 / 359595 > Fax: ++44(0)1932 357873 > > mailto:j.d.tucker at vla.defra.gsi.gov.uk > > > > > > > > Veterinary Laboratories Agency (VLA) > > This email and any attachments is intended for the named recipient only. > Its > unauthorised use, disclosure, storage or copying is not permitted. If you > have > received it in error, please destroy all copies and inform the sender. Whilst > this > email and associated attachments will have been checked for known viruses > whilst within VLA systems we can accept no responsibility once it has left > our > systems. Communications on VLA's computer systems may be monitored > and/or recorded to secure the effective operation of the system and for > other > lawful purposes. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From fmr at sfu.ca Thu Feb 5 12:41:18 2004 From: fmr at sfu.ca (Fiona Roche) Date: 05 Feb 2004 09:41:18 -0800 Subject: [BiO BB] (no subject) In-Reply-To: <104FE795DA19D411A71A0008C733F76404A43BCB@vla6> References: <104FE795DA19D411A71A0008C733F76404A43BCB@vla6> Message-ID: <1076002912.1352.1162.camel@localhost.localdomain> > I'm looking for software that will indicate if I have a secretion protein or > not. Check out PSORTB, a tool which predicts the subcellular localization of a protein from its sequence. The current version handles protein sequences from Gram-negative bacteria only however, a newer version for Gram positives is in the pipeline. http://www.psort.org/psortb/index.html Fiona > I'm also looking for some software that will find cleavage site within my > seq. > Any suggestions ?? > Regards > James > James Tucker > Brucella Research Group > Department of Bacterial Diseases > VLA Weybridge > Woodham Lane > New Haw > Addlestone > Surrey > KT15 3NB > > Tel: ++44(0)1932 357227 / 359595 > Fax: ++44(0)1932 357873 > > mailto:j.d.tucker at vla.defra.gsi.gov.uk > > > > > > > > Veterinary Laboratories Agency (VLA) > > This email and any attachments is intended for the named recipient only. Its > unauthorised use, disclosure, storage or copying is not permitted. If you have > received it in error, please destroy all copies and inform the sender. Whilst this > email and associated attachments will have been checked for known viruses > whilst within VLA systems we can accept no responsibility once it has left our > systems. Communications on VLA's computer systems may be monitored > and/or recorded to secure the effective operation of the system and for other > lawful purposes. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Fiona Roche, PhD MBB, Brinkman Lab, Simon Fraser University, Burnaby, British Columbia, Canada Phone: (001)-604-291-4206 Email: fmr at sfu.ca From cmoita at igc.gulbenkian.pt Thu Feb 5 16:21:09 2004 From: cmoita at igc.gulbenkian.pt (Catarina S. F. Moita) Date: Thu, 5 Feb 2004 21:21:09 -0000 (WET) Subject: [BiO BB] Re: BiO_Bulletin_Board digest - James Tucker In-Reply-To: <20040205170243.5B63DD1F1B@www.bioinformatics.org> References: <20040205170243.5B63DD1F1B@www.bioinformatics.org> Message-ID: <3113.213.13.51.139.1076016069.squirrel@webmail.igc.gulbenkian.pt> > When replying, PLEASE edit your Subject line so it is more specific > than "Re: BiO_Bulletin_Board digest, Vol..." And, PLEASE delete any > unrelated text from the body. > Message: 3 > From: "Tucker, James" > To: "'bio_bulletin_board at bioinformatics.org'" > > Date: Thu, 5 Feb 2004 14:29:36 -0000 > Subject: [BiO BB] (no subject) > Reply-To: bio_bulletin_board at bioinformatics.org > Dear James, Take a look to SignalP 2.0.... http://www.cbs.dtu.dk/services/SignalP-2.0/#submission Best regards, Catarina. > Hi all, > I'm looking for software that will indicate if I have a secretion protein > or > not. > I'm also looking for some software that will find cleavage site within my > seq. > Any suggestions ?? > Regards > James > James Tucker > Brucella Research Group > Department of Bacterial Diseases > VLA Weybridge > Woodham Lane > New Haw > Addlestone > Surrey > KT15 3NB > > Tel: ++44(0)1932 357227 / 359595 > Fax: ++44(0)1932 357873 > > mailto:j.d.tucker at vla.defra.gsi.gov.uk > > > > > > > > Veterinary Laboratories Agency (VLA) > > This email and any attachments is intended for the named recipient only. > Its > unauthorised use, disclosure, storage or copying is not permitted. If you > have > received it in error, please destroy all copies and inform the sender. > Whilst this > email and associated attachments will have been checked for known viruses > whilst within VLA systems we can accept no responsibility once it has left > our > systems. Communications on VLA's computer systems may be monitored > and/or recorded to secure the effective operation of the system and for > other > lawful purposes. > From S99007386 at student.usp.ac.fj Thu Feb 5 20:42:42 2004 From: S99007386 at student.usp.ac.fj (Sunil Raj Prasad) Date: Fri, 06 Feb 2004 13:42:42 +1200 Subject: [BiO BB] cluster analysis software Message-ID: <20040206014405.949E76000B@mx2.usp.ac.fj> Dear Christophe Battail, I am a Masters Student at the University of the South Pacific in Fiji and am studying the leaf litter invertebrates. My project involves using the litter invertebrates (opliones, Staphylinids and Weevils) to map their biodiversity hotspots. I extract the invertebrates using the Winkler Sacks and then sort them into different morphospecies based on characters derived from literature and also from consultation of prominent scientist in these field. I am at the moment using the Jaccard?s index to calculated the similarity between the different sites and this will help me map biological provinces in Fiji where really unique, or unique enough for conservation purposes, litter invertebrates exist. It is known that invertebrates tend to be more localized then other frequently studied fauna such as Birds, Mammals, Hepeto fauna, etc. Therefore, this data together with data derived from other studies will be used to map high biodiversity regions within Fiji (including the major islands and the other outer islands). I also want to do Complementarity analysis and cluster analysis to map their relatedness based on the morphological characters. However, I do not know of any such software program which can do that. However, I have surfed the net band have indeed found several packages which do cluster analysis based on genetics. I want to do these relatedness analysis based on the morphological characters instead of the genetics. Do you know of any such packages or if it is available on the net for me to download. Please let me know of any fees in advance. With kind regards, Sunil Raj Prasad, GA Conservation Biology, Biology Department, SPAS, University of the South Pacific, Fiji Islands. (679) 3311061 sunilrajprasad at hotmail.com s99007386 at student.usp.ac.fj From ISivaram at wockhardtin.com Thu Feb 5 23:49:29 2004 From: ISivaram at wockhardtin.com (ISivaram at wockhardtin.com) Date: Fri, 6 Feb 2004 10:19:29 +0530 Subject: [BiO BB] Secretory protein and cleavage site Message-ID: Hi check out SignalP and Target P at http://www.cbs.dtu.dk/services/ and also PSORT server for cleavage site check this out http://us.expasy.org/tools/#proteome Hope this will help u Regards sivaram From combiofriends at yahoo.com Fri Feb 6 07:15:39 2004 From: combiofriends at yahoo.com (com bio) Date: Fri, 6 Feb 2004 04:15:39 -0800 (PST) Subject: [BiO BB] (no subject) Message-ID: <20040206121539.67848.qmail@web61101.mail.yahoo.com> hello, we have created many functions that are often used in genome analysis.we want to make a open library out of it. plz guide us how to go about we used borland c++ deepan ===== ------------------------------------------- center for biotechnology anna university chennai-25 india __________________________________ Do you Yahoo!? Yahoo! Finance: Get your refund fast by filing online. http://taxes.yahoo.com/filing.html From lxyiwc at yahoo.com Fri Feb 6 20:13:56 2004 From: lxyiwc at yahoo.com (l x yi) Date: Fri, 6 Feb 2004 17:13:56 -0800 (PST) Subject: [BiO BB] using protein databases Message-ID: <20040207011356.90248.qmail@web21204.mail.yahoo.com> Hi, I'm a new user of protein databases, could someone help me with a few questions? 1. can anyone tell me how to download 200 random sequences of length >150 from a reliable protein database? 2. For the profiles in pfam, if there are gaps between two continuoud patterns, does it make sense to search only one of the pattern? Is it correct the whole thing is a domain, and the patterns seperated by the gaps are motifs? 3. also, in pfam, the uk site http://www.sanger.ac.uk/Software/Pfam/data/jtml/seed/PF00047.shtml i got results like PIGR_HUMAN/33-112 GNSVSITCYYP.........PTSVNRHTRKYWCR....QGARGGCITLISSEGYVSSK............YAGRANLTNF O60667/30-106 GGSVTIKCPLP.............EMHVRIYLC.......REMAGSGTCGTVVSTTNFIK........AEYKGRVTLKQY TVA1_HUMAN/35-113 KEDVTLDCVYE...........TRDTTYYLFWY.......KQPPSGELVFLIRRNSFDEQ........NEISGRYSWNFQ TVA1_MOUSE/35-112 GASLQLRCKYS............YSATPYLFWY.......VQYPRQGLQLLLKYYSGDPV........VQGVNGFEAEFS TVA1_MOUSE/35-112-SS TSCEEECCCEC............CSSCCEEEEE.......EECTTCCCEEEEEECSSCSE........EECTTTCEEEEE TVA1_MOUSE/35-112-SA 43603040406............2735020000.......01275521531041246633........172675040511 TVA2_MOUSE/36-111 GARTSLNCTFS............DSASQYFWWY.......RQHSGKAPKALMSIFSNGE..........KEEGRFTIHLN TVB1_MOUSE/35-113 GQKAKMRCIPE.............KGHPVVFWY.......QQNKNNEFKFLINFQNQEVLQ......QIDMTEKRFSAEC TVB7_MOUSE/35-113 GQEATLWCEPI.............SGHSAVFWY.......RQTIVQGLEFLTYFRNQAPID......DSGMPKERFSAQM TCB_FLV/44-121 GQQVTLSCFPI.............SGHLSLYWY.......QQAVGQGPQLLIQYYNREER.......GKGNFPERFSAQQ what does the numbers on line 6 mean? thanks very much. Lily --------------------------------- Do you Yahoo!? Yahoo! Finance: Get your refund fast by filing online -------------- next part -------------- An HTML attachment was scrubbed... URL: From nrballor at mtu.edu Mon Feb 9 10:30:56 2004 From: nrballor at mtu.edu (Nicholas R. Ballor) Date: Mon, 9 Feb 2004 10:30:56 -0500 Subject: [BiO BB] Ferrous Iron Binding Motif Message-ID: <000101c3ef21$b61d5240$b250db8d@NBALLOR> Hey Everyone, I am trying to find proteins in a prokaryotic organism that are capable of binding ferrous iron (Fe2+). To do this, I need a sequence (amino acid residue or nucleotide) corresponding to a ferrous iron binding motif so that I can begin searching for proteins in the organism of interest. I am looking for an active site (a motif) involved in the specific binding of ferrous iron (possibly divalent ions in general) whose purpose is to recruit the iron for the cell. Does anyone know of any motifs involved in binding ferrous iron, or how to best approach the search? To give an idea of what I'm looking for, chemicals/peptides serving a similar purpose include transferrins. Thanks in advance, nrballor -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgollery at unr.edu Mon Feb 9 14:05:29 2004 From: mgollery at unr.edu (Martin Gollery) Date: Mon, 9 Feb 2004 11:05:29 -0800 Subject: [BiO BB] Ferrous Iron Binding Motif In-Reply-To: <000101c3ef21$b61d5240$b250db8d@NBALLOR> References: <000101c3ef21$b61d5240$b250db8d@NBALLOR> Message-ID: <1076353529.4027d9f98ef30@webmail.unr.edu> Check out the Prosite motif PDOC00462 - is this what you have in mind? Marty Quoting "Nicholas R. Ballor" : > Hey Everyone, > > I am trying to find proteins in a prokaryotic organism that are capable > of binding ferrous iron (Fe2+). To do this, I need a sequence (amino > acid residue or nucleotide) corresponding to a ferrous iron binding > motif so that I can begin searching for proteins in the organism of > interest. I am looking for an active site (a motif) involved in the > specific binding of ferrous iron (possibly divalent ions in general) > whose purpose is to recruit the iron for the cell. Does anyone know of > any motifs involved in binding ferrous iron, or how to best approach the > search? > > To give an idea of what I'm looking for, chemicals/peptides serving a > similar purpose include transferrins. > > Thanks in advance, > > nrballor > Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From forward at hongyu.org Mon Feb 9 14:26:46 2004 From: forward at hongyu.org (Hongyu Zhang) Date: Mon, 9 Feb 2004 11:26:46 -0800 Subject: [BiO BB] protein clustering threshold Message-ID: <1076354806.4027def609dbd@hongyu.org> Does anyone have examples of two proteins with >90% sequence identity have differenct functions? I need it as a proof to cluster a protein sequence library. Thanks! Hongyu From dmb at mrc-dunn.cam.ac.uk Mon Feb 9 16:02:44 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 9 Feb 2004 21:02:44 +0000 (GMT) Subject: [BiO BB] protein clustering threshold In-Reply-To: <1076354806.4027def609dbd@hongyu.org> Message-ID: I heard about an enzyme where a single amino acid change alters substrate specificity. Also, mutating an active site residue will distroy function. When clustering I always keep mappings to the cluster members (groupies), so you can assess things like functional annotations / species distributions within clusters. The best reason for clustering I know is to improve sequence search statistics and speed without sacrificing coverage, if you are looking for genuine 'biological' non redundancy use refSeq or similar (if possible). It should be very easy for you to get lots of examples from the following file... ftp://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref90/uniref90.xml.gz It contains XML format 'cluster' data for Swiss Prot + TrEMBL records derived from CD-HIT. I have an example XML parser in perl if you need help parsing this file. Using this you could easily pull out cluster members (at 90%) with different EC numbers as annotated in Swiss Prot. Actually this information should be quite useful for the annotators. You just made me curious... Here is a (bad) example... +--------+-----------------------------------------+-----------+--------+ | accn | name | ec | rep | +--------+-----------------------------------------+-----------+--------+ | P70694 | Estradiol 17 beta-dehydrogenase 5 | 1.1.1.- | P51857 | | P52895 | Aldo-keto reductase family 1 member C2 | 1.1.1.- | P51857 | | P52895 | Aldo-keto reductase family 1 member C2 | 1.3.1.20 | P51857 | | Q04828 | Aldo-keto reductase family 1 member C1 | 1.1.1.- | P51857 | | Q04828 | Aldo-keto reductase family 1 member C1 | 1.3.1.20 | P51857 | | P42330 | Aldo-keto reductase family 1 member C3 | 1.1.1.- | P51857 | | P42330 | Aldo-keto reductase family 1 member C3 | 1.1.1.188 | P51857 | | P42330 | Aldo-keto reductase family 1 member C3 | 1.3.1.20 | P51857 | | P80508 | Prostaglandin-E2 9-reductase | 1.1.1.149 | P51857 | | P80508 | Prostaglandin-E2 9-reductase | 1.1.1.189 | P51857 | | P23457 | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | P51857 | | P05980 | Prostaglandin-F synthase 1 | 1.1.1.188 | P51857 | | P52897 | Prostaglandin-F synthase 2 | 1.1.1.188 | P51857 | | P17516 | Aldo-keto reductase family 1 member C4 | 1.1.1.- | P51857 | | P17516 | Aldo-keto reductase family 1 member C4 | 1.1.1.225 | P51857 | | P17516 | Aldo-keto reductase family 1 member C4 | 1.1.1.50 | P51857 | | Q8VC28 | Aldo-keto reductase family 1 member C13 | 1.1.1.- | P51857 | | P51652 | 20-alpha-hydroxysteroid dehydrogenase | 1.1.1.149 | P51857 | | P31210 | 3-oxo-5-beta-steroid 4-dehydrogenase | 1.3.99.6 | P51857 | | P52898 | Dihydrodiol dehydrogenase 3 | 1.-.-.- | P51857 | +--------+-----------------------------------------+-----------+--------+ Is this showing up a complex cluster? Ta, Dan. P.S. The above cluster file isn't enough to get this data, you need the full Uniprot data set. I am using a rough sql schema of my own design built using (copying) swissknife - anyone know how to change the XML schema for the XML file into an SQL schema? Should I just use XML SQL? On Mon, 9 Feb 2004, Hongyu Zhang wrote: > > > Does anyone have examples of two proteins with >90% > sequence identity have differenct functions? I need it as a > proof to cluster a protein sequence library. > > Thanks! > > Hongyu > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From e_hongyu at yahoo.com Fri Feb 6 18:12:45 2004 From: e_hongyu at yahoo.com (Hongyu Zhang) Date: Fri, 6 Feb 2004 15:12:45 -0800 (PST) Subject: [BiO BB] protein clustering threshold Message-ID: <20040206231245.30787.qmail@web12603.mail.yahoo.com> Does anyone have examples of two proteins with >90% identity have differenct functions? I need it as a proof to cluster a protein sequence library. Thanks! Hongyu __________________________________ Do you Yahoo!? Yahoo! Finance: Get your refund fast by filing online. http://taxes.yahoo.com/filing.html From jeff at bioinformatics.org Mon Feb 9 20:49:25 2004 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 09 Feb 2004 20:49:25 -0500 Subject: [BiO BB] ANNOUNCE: 4th Annual Meeting of Bioinformatics.Org Message-ID: <402838A5.5040302@bioinformatics.org> ANNOUNCING THE 4TH ANNUAL MEETING OF THE BIOINFORMATICS ORGANIZATION, INC. (BIOINFORMATICS.ORG) MARCH 30 - APRIL 1, 2004 AT THE BIO-IT WORLD CONFERENCE + EXPO HYNES CONVENTION CENTER BOSTON, MASSACHUSETTS, USA Bioinformatics.Org will be holding its fourth Annual Meeting this spring. All are invited to attend. This year, the meeting will be held in conjuction with the Bio-IT World Conference + Expo in Boston. Our participation includes the co-organization of the Bioclusters Workshop (March 30, all day), presentation of the 2004 Benjamin Franklin Award in Bioinformatics (March 31, 8:30 AM), and a reception where new features and resources will be announced (date/time TBA). Bio-IT World is offering a registration discount for all members of Bioinformatics.Org. Those who register online at http://www.bio-itworldexpo.com/ by February 27, 2004 will receive a 25% discount off all early bird conference packages to the Bio-IT World Conference + Expo. To receive the 25% discount, please register online by February 27, 2004 with the exclusive Bioinformatics.Org member PRIORITY CODE: BTA2. More information on the event has been provided by Bio-IT World below: For the 3rd consecutive year, Bio-IT World Conference + Expo(tm) returns to Boston's Hynes Convention Center, March 30 - April 1, 2004 and online registration is now open. By attending the conference program, you will learn even more on the technological advances in drug discovery and delivery than ever before. You'll take back valuable tips on how to make your job easier and your company more profitable. Read on to see how... Collaboration with several leading industry partners such as Bio-IT World magazine, Thomson CenterWatch, Medical Records Institute (MRI), Bioinformatics.Org, Ernst & Young, IDC and IDG Ventures will provide you with educational content found at no other event. HERE IS WHAT YOU HAVE TO LOOK FORWARD TO! ============================================================== IN-DEPTH WORKSHOPS Offering you the opportunity to quickly become more knowledgeable on a specialized topic such as Bioclusters, Life Science Identifiers (LSID), Document Management and Regulatory Compliance, Systems Biology and Conducting a BioLaw and Business Strategic Audit (tm). http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10139&p_navID=18 THE DRUGGABLE GENOME This two day track will help you identify promising new drug targets and prioritize leads, diagnose high-risk individuals and populations, and apply an army of in silico and laboratory tools to harness this knowledge to rationally design drugs and expedite their development all through the use of technology. http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10014&p_navID=18#track1 INFORMATICS & IT INFRASTRUCTURE By attending these sessions you will be able to combat the new challenges that are associated with data management and computational workflows with enabling technologies, both software and hardware. Due to the critical nature of these advances in supercomputing and informatics, you need to stay up-to-date for the success of your research and development initiatives. Sponsored by Netezza http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10014&p_navID=18#track2 E-CLINICAL TRIALS RESEARCH You may be currently facing rising costs, intense competition, regulatory pressures and shortages of qualified professionals and patients. Bio-IT World Conference will provide you with the essential information on ways to streamline performance, increase efficiency, coordinate patient recruitment and record-keeping, and improve regulatory compliance. Co-Chaired by Thomson CenterWatch http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10014&p_navID=18#track3 CO-LOCATED HEALTH-IT WORLD CONFERENCE Join hospitals and clinical centers nationwide who have been implementing mobile devices, electronic medical records and computer physician order entry technologies and more which have made significant impacts on the doctor/patient relationship, efficiencies, return on investments and patient safety issues. Co-Chaired by Medical Records Institute and Health-IT World. http://www.health-itworldexpo.com/healthworldexpo/V40/index.cvn?id=10180&p_navID=18 KEYNOTES http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10146&p_navID=115 ============================================================== * Dr. George Poste, Healthcare Networks * Dr. Susan L. Linquist, Whitehead Institute for Biomedical Research * Michael C. Ruettgers, EMC * Steven H. Holtzman, Infinity Pharmaceuticals * Dr. Peter L. Elkin, Mayo Medical School * Dr. John Parrish, The Center for the Integration of Medicine and Innovative Technology (CIMIT) SPECIAL CONFERENCE + EXPO EVENTS! http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10182&p_navID=107 ============================================================== * Ernst & Young Venture Summit sponsored by IDG Ventures * Opening Night Networking Reception * Benjamin Franklin Award sponsored by Bionformatics.Org * Bio-IT World Best of Show Award * Over 90 companies showcasing the best solutions * Technology Showcase Presentations * Birds-of-a-Feather Meetings * BiotechTuesday Networking Event * Featured Track Speakers and Internationally Recognized Faculty DOWNLOAD THE CONFERENCE BROCHURE FOR FULL EVENT DETAILS ============================================================== http://www.bioitworldexpo.com/convdata/boston03/brochures/Bio-IT%20World%20Conference%20+%20Expo%20FINAL%20Brochure.pdf We look forward to seeing you in March. All registration fees are non-refundable, including all cancellations, and credentials are transferable. This offer/discount is valid for one new registration only and must be redeemed/noted at time of initial registration. No refunds or credits will be issued for a discount after the initial registration. This offer cannot be duplicated, redeemed for cash, or used in conjunction with any other offer. Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org President, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From Alex.Bossers at wur.nl Tue Feb 10 02:04:25 2004 From: Alex.Bossers at wur.nl (Bossers, Alex) Date: Tue, 10 Feb 2004 08:04:25 +0100 Subject: [BiO BB] protein clustering threshold Message-ID: <839C6D97DA4B564882F385F1DA46742C01C0FC31@slely0004.wurnet.nl> Hi, And then there were...... prions. Proteins with the same primary amino acid sequence but different conformations and functions....... Most of you know of prions and prion proteins in infectious diseases like mad-cow disease (BSE) and CJD in humans. Some info at: http://home.hccnet.nl/a.bossers/Thesis.htm Alex > -----Oorspronkelijk bericht----- > Van: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board- > admin at bioinformatics.org] Namens Hongyu Zhang > Verzonden: maandag 9 februari 2004 20:27 > Aan: bio_bulletin_board at bioinformatics.org > Onderwerp: [BiO BB] protein clustering threshold > > > > Does anyone have examples of two proteins with >90% > sequence identity have differenct functions? I need it as a > proof to cluster a protein sequence library. > > Thanks! > > Hongyu > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From B.A.T.Svensson at lumc.nl Tue Feb 10 03:03:45 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Tue, 10 Feb 2004 09:03:45 +0100 Subject: [BiO BB] protein clustering threshold Message-ID: Do you include point mutations? -----Original Message----- From: Hongyu Zhang To: bio_bulletin_board at bioinformatics.org Sent: 2004-02-09 20:26 Subject: [BiO BB] protein clustering threshold Does anyone have examples of two proteins with >90% sequence identity have differenct functions? I need it as a proof to cluster a protein sequence library. Thanks! Hongyu _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From idoerg at burnham.org Tue Feb 10 12:20:43 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 10 Feb 2004 09:20:43 -0800 Subject: [BiO BB] protein clustering threshold In-Reply-To: <20040206231245.30787.qmail@web12603.mail.yahoo.com> Message-ID: Not to answer your question directly, just to add confusion: How about the same protein which performs different functions? Crystallins are an example of a protease which, in the eye lens, serves as a transparent buffer. There are other such "moonlighting proteins" look at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12902157&dopt=Abstract ./I -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo On Fri, 6 Feb 2004, Hongyu Zhang wrote: > Does anyone have examples of two proteins with >90% > identity have differenct functions? I need it as a > proof to cluster a protein sequence library. > > Thanks! > > Hongyu > > __________________________________ > Do you Yahoo!? > Yahoo! Finance: Get your refund fast by filing online. > http://taxes.yahoo.com/filing.html > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From hamid at ibb.ut.ac.ir Tue Feb 10 17:10:31 2004 From: hamid at ibb.ut.ac.ir (hamid) Date: Wed, 11 Feb 2004 01:40:31 +0330 Subject: [BiO BB] Ferrous Iron Binding Motif In-Reply-To: <000101c3ef21$b61d5240$b250db8d@NBALLOR> References: <000101c3ef21$b61d5240$b250db8d@NBALLOR> Message-ID: Check this database: go to: http://bioinformatics.ut.ac.ir then go to services page then click on PSSD database then and enter this keyword in compound field and do search :"Ferrochelatase" /* ?Hamid Nikbakht, ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?M.Sc of Cell and Molecular Biology, ? ? ? ? ? ? ?Laboratory of Biophysics and Molecular Biology, ?Institute of Biochemistry and Biophysics(IBB), ?University of Tehran, ? ? ? ? ? ? ? ? ? ? ? ? ? ?Tehran,Iran. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Tel: +98-21-611-3322 ? ? ? ? ? ? ? ? ? ? ? ? ? ?Fax: +98-21-640-4680 ? ? ? ? ? ? ? ? ? ? ? ? ? ?E-Mail: hamid at ibb.ut.ac.ir ? ? ? ? ? ? ? ? ? ? ?Alt. E-mail: nikbakht at ibb.ut.ac.ir ? ? ? ? ? ? */ From mgollery at unr.edu Tue Feb 10 21:06:27 2004 From: mgollery at unr.edu (Martin Gollery) Date: Tue, 10 Feb 2004 18:06:27 -0800 Subject: [BiO BB] Interview request for biotech book In-Reply-To: References: Message-ID: <1076465187.40298e23671ac@webmail.unr.edu> Yes, you can give me a call tomorrow. Marty Quoting CAROLE S MOUSSALLI : > > ------=_NextPart_001_00C3_01C3DE9D.63D01980 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Greetings to all super-busy, much-in-demand bioinformatics = > professionals: > =20 > I am a recent graduate of Columbia Business School and have been = > commissioned by Vault, Inc. to write a career development guide on the = > Biotech industry for early to mid-career professionals. > =20 > I need help identifying someone who is willing to speak with me for = > approx. 45 minutes for a Day-in-the-Life=20 > interview. Questions and format is set; full confidentiality is = > assured. Samples of similar profiles are available. > =20 > The best candidate will have been on the job for 1-3 years and have = > graduated with a degree in bioinformatics. > =20 > On behalf of my publisher, I would like to thank everyone who can give = > me some time and attention. > > Kind Regards, > > Carole > > Carole S. Moussalli > cmoussalli03 at gsb.columbia.edu > 23 Maplewood Street > Watertown, MA 02472-3501 > Tel: 617-926-6782 > Fax: 617-926-6783 > Cell: 917-667-6186 > > ------=_NextPart_001_00C3_01C3DE9D.63D01980 > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > content=3Dtext/html;charset=3Diso-8859-1> > > > > style=3D"PADDING-LEFT: 30px; FONT-WEIGHT: normal; FONT-SIZE: 10pt; = > COLOR: #000000; BORDER-TOP-STYLE: none; PADDING-TOP: 20px; FONT-STYLE: = > normal; FONT-FAMILY: Arial; BORDER-RIGHT-STYLE: none; BORDER-LEFT-STYLE: = > none; TEXT-DECORATION: none; BORDER-BOTTOM-STYLE: none"=20 > bgColor=3D#ffffff leftMargin=3D0=20 > background=3Dcid:00c101c3dec7$4c93d200$6501a8c0 at carole2y0qka5i = > topMargin=3D0=20 > acc_role=3D"text" CanvasTabStop=3D"true" name=3D"Compose message = > area"> >
Greetings to all super-busy, much-in-demand=20 > bioinformatics professionals:
 
I am a recent graduate = > of=20 > Columbia Business School and have been commissioned by Vault, Inc. = > to write=20 > a career development guide on the Biotech industry for early to = > mid-career=20 > professionals.
 
I need help identifying someone who is = > willing to=20 > speak with me for approx. 45 minutes for a=20 > Day-in-the-Life 
interview.  Questions and format is set;=20 > full confidentiality is assured.  Samples of similar = > profiles are=20 > available.
 
The best candidate will have been on the job for = > 1-3=20 > years and have graduated with a degree in = > bioinformatics.
 
On=20 > behalf of my publisher, I would like to thank everyone who can give me = > some time=20 > and attention.

Kind Regards,
>
 
>
size=3D4>Carole
>

Carole S. Moussalli
href=3D"mailto:cmoussalli03 at gsb.columbia.edu">cmoussalli03 at gsb.columbia.e= > du
23=20 > Maplewood Street
Watertown, MA  02472-3501
Tel: =20 > 617-926-6782
Fax:  617-926-6783
Cell:=20 > 917-667-6186
> > ------=_NextPart_001_00C3_01C3DE9D.63D01980-- > Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From forward at hongyu.org Tue Feb 10 20:58:20 2004 From: forward at hongyu.org (Hongyu Zhang) Date: Tue, 10 Feb 2004 17:58:20 -0800 Subject: [BiO BB] protein clustering threshold Message-ID: <1076464700.40298c3c1fbe2@hongyu.org> I also remember hearing from somewhere that a single mutation at active sites can change the activity of a protein from catalyzing one reaction to another. I need to find the the exact example. Can anyone help me, please? I don't think Prion is a good example, because my question is not about whether one protein can have multiple functions. Dan, thanks for the Uniprot example, but I found that some of the pair-wise percentages of identities within the cluster are far less than 90% (e.g., between representative P51857 and member P52895 is 57.3% based on CLUSTALW). I think it was caused by the clustering algorithm used in the data set. Another problem in the UniRef90 XML file is that it doesn't come with Evidence code, which makes it hard to tell whether the annotations are from experimental results or electronic annotations. The latest TrEMBL provides this evidence code, which I am going to give a try. I will keep you guys posted. BTW, I also have a Perl XML parser, which is based on the XML::Twig module, but I am not familiar with the automatic conversion between XML schema and SQL tables. Thanks again. --Hongyu From dmb at mrc-dunn.cam.ac.uk Tue Feb 10 21:21:46 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 11 Feb 2004 02:21:46 +0000 (GMT) Subject: [BiO BB] protein clustering threshold In-Reply-To: <1076464700.40298c3c1fbe2@hongyu.org> Message-ID: On Tue, 10 Feb 2004, Hongyu Zhang wrote: > I also remember hearing from somewhere that a single mutation at active sites > can change the activity of a protein from catalyzing one reaction to another. > I need to find the the exact example. Can anyone help me, please? I don't think > Prion is a good example, because my question is not about whether one protein > can have multiple functions. I think the above 'infamous' example was actualy engineered, rather than existing naturally. > Dan, thanks for the Uniprot example, but I found that some of the pair-wise > percentages of identities within the cluster are far less than 90% (e.g., > between representative P51857 and member P52895 is 57.3% based on CLUSTALW). I Sorry! My fault - I was using UniRef50! > think it was caused by the clustering algorithm used in the data set. Another > problem in the UniRef90 XML file is that it doesn't come with Evidence code, > which makes it hard to tell whether the annotations are from experimental > results or electronic annotations. The latest TrEMBL provides this evidence Yup, this is why you need to link to main record data somehow. > code, which I am going to give a try. I will keep you guys posted. BTW, I also > have a Perl XML parser, which is based on the XML::Twig module, but I am not I am not sure if this works on massive XML files, but maby it is OK if you are only looking at a few identifiers. > familiar with the automatic conversion between XML schema and SQL tables. I posted a question at comp.text.xml, so I will let you know what results I get back (if any!). Cheers, Dan. > Thanks again. > > --Hongyu > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From Alex.Bossers at wur.nl Wed Feb 11 02:37:59 2004 From: Alex.Bossers at wur.nl (Bossers, Alex) Date: Wed, 11 Feb 2004 08:37:59 +0100 Subject: [BiO BB] protein clustering threshold Message-ID: <839C6D97DA4B564882F385F1DA46742C01DE5F35@slely0004.wurnet.nl> Hhhhhhmmmm in addition: in prions a single polymorphism can determine species specificity. Even within species a single poly can determine the specificity of prion conversion reactions.... Just a thought, NOT to confuse........ Alex > -----Oorspronkelijk bericht----- > Van: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board- > admin at bioinformatics.org] Namens Hongyu Zhang > Verzonden: woensdag 11 februari 2004 2:58 > Aan: bio_bulletin_board at bioinformatics.org > Onderwerp: Re: [BiO BB] protein clustering threshold > > I also remember hearing from somewhere that a single mutation at active sites > can change the activity of a protein from catalyzing one reaction to another. > I need to find the the exact example. Can anyone help me, please? I don't think > Prion is a good example, because my question is not about whether one protein > can have multiple functions. > > Dan, thanks for the Uniprot example, but I found that some of the pair-wise > percentages of identities within the cluster are far less than 90% (e.g., > between representative P51857 and member P52895 is 57.3% based on > CLUSTALW). I > think it was caused by the clustering algorithm used in the data set. Another > problem in the UniRef90 XML file is that it doesn't come with Evidence code, > which makes it hard to tell whether the annotations are from experimental > results or electronic annotations. The latest TrEMBL provides this evidence > code, which I am going to give a try. I will keep you guys posted. BTW, I also > have a Perl XML parser, which is based on the XML::Twig module, but I am not > familiar with the automatic conversion between XML schema and SQL tables. > > Thanks again. > > --Hongyu > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From szed4 at yahoo.com Wed Feb 11 13:04:39 2004 From: szed4 at yahoo.com (Shamshad Zarina) Date: Wed, 11 Feb 2004 10:04:39 -0800 (PST) Subject: [BiO BB] protein clustering threshold In-Reply-To: Message-ID: <20040211180439.21480.qmail@web14002.mail.yahoo.com> Crystallins are very good examples for proteins having structural and sequence similarity but different functions. I work on lens protiens but I don't recall an example with >90% identity yet different functions. One example with less identity is of Rho-crystallin found in bull-frog where it acts as 'structural protein' to maintain lens transparency. It shows 55% sequence identity with Aldo-keto reductase superfamily which are enzymes. Both proteins have similar three dimensioanl structure and one residue required for catalytic activity is absent in rho-crystallin. Best, Shamshad --- Iddo Friedberg wrote: > Not to answer your question directly, > just to add confusion: > > How about the same protein which performs different > functions? > Crystallins > are an example of a protease which, in the eye lens, > serves as a > transparent buffer. > > There are other such "moonlighting proteins" look > at: > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12902157&dopt=Abstract > > ./I > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037, USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 646 3171 > http://ffas.ljcrf.edu/~iddo > > On Fri, 6 Feb 2004, Hongyu Zhang wrote: > > > Does anyone have examples of two proteins with > >90% > > identity have differenct functions? I need it as a > > proof to cluster a protein sequence library. > > > > Thanks! > > > > Hongyu > > > > __________________________________ > > Do you Yahoo!? > > Yahoo! Finance: Get your refund fast by filing > online. > > http://taxes.yahoo.com/filing.html > > _______________________________________________ > > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________ Do you Yahoo!? Yahoo! Finance: Get your refund fast by filing online. http://taxes.yahoo.com/filing.html From idoerg at burnham.org Wed Feb 11 13:23:26 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 11 Feb 2004 10:23:26 -0800 Subject: [BiO BB] protein clustering threshold In-Reply-To: <20040211180439.21480.qmail@web14002.mail.yahoo.com> References: <20040211180439.21480.qmail@web14002.mail.yahoo.com> Message-ID: <402A731E.2060108@burnham.org> Shamshad: Turkey delta-crystallin has a 90% ID w/ argininosuccinate lyase. See: NATURE Structural Biology, vol.1, No.10, Pp724-733, October, 1994 A.Simpson, et al. `The structure of avian eye lens delta crystallin reveals a new fold for a superfamily of oligomeric enzymes' Iddo Shamshad Zarina wrote: > Crystallins are very good examples for proteins having > structural and sequence similarity but different > functions. I work on lens protiens but I don't recall > an example with >90% identity yet different functions. > > > One example with less identity is of Rho-crystallin > found in bull-frog where it acts as 'structural > protein' to maintain lens transparency. It shows 55% > sequence identity with Aldo-keto reductase superfamily > which are enzymes. Both proteins have similar three > dimensioanl structure and one residue required for > catalytic activity is absent in rho-crystallin. > > Best, > Shamshad > > --- Iddo Friedberg wrote: > >>Not to answer your question directly, >>just to add confusion: >> >>How about the same protein which performs different >>functions? >>Crystallins >>are an example of a protease which, in the eye lens, >>serves as a >>transparent buffer. >> >>There are other such "moonlighting proteins" look >>at: >> > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12902157&dopt=Abstract > >>./I >> >>-- >>Iddo Friedberg, Ph.D. >>The Burnham Institute >>10901 N. Torrey Pines Rd. >>La Jolla, CA 92037, USA >>Tel: +1 (858) 646 3100 x3516 >>Fax: +1 (858) 646 3171 >>http://ffas.ljcrf.edu/~iddo >> >>On Fri, 6 Feb 2004, Hongyu Zhang wrote: >> >> >>>Does anyone have examples of two proteins with >>>90% >>>identity have differenct functions? I need it as a >>>proof to cluster a protein sequence library. >>> >>>Thanks! >>> >>>Hongyu >>> >>>__________________________________ >>>Do you Yahoo!? >>>Yahoo! Finance: Get your refund fast by filing >> >>online. >> >>>http://taxes.yahoo.com/filing.html >>>_______________________________________________ >>>BiO_Bulletin_Board maillist - >> >>BiO_Bulletin_Board at bioinformatics.org >> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >>_______________________________________________ >>BiO_Bulletin_Board maillist - >>BiO_Bulletin_Board at bioinformatics.org >> > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > __________________________________ > Do you Yahoo!? > Yahoo! Finance: Get your refund fast by filing online. > http://taxes.yahoo.com/filing.html > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From szed4 at yahoo.com Thu Feb 12 12:03:37 2004 From: szed4 at yahoo.com (Shamshad Zarina) Date: Thu, 12 Feb 2004 09:03:37 -0800 (PST) Subject: [BiO BB] protein clustering threshold In-Reply-To: <402A731E.2060108@burnham.org> Message-ID: <20040212170337.31867.qmail@web14001.mail.yahoo.com> Thanks, Iddo. This might be the example Hongyu is looking for. Shamshad --- Iddo Friedberg wrote: > Shamshad: > > Turkey delta-crystallin has a 90% ID w/ > argininosuccinate lyase. See: > > NATURE Structural Biology, vol.1, No.10, Pp724-733, > October, 1994 > A.Simpson, et al. > `The structure of avian eye lens delta crystallin > reveals a new fold for > a superfamily of oligomeric enzymes' > > > Iddo > > Shamshad Zarina wrote: > > Crystallins are very good examples for proteins > having > > structural and sequence similarity but different > > functions. I work on lens protiens but I don't > recall > > an example with >90% identity yet different > functions. > > > > > > One example with less identity is of > Rho-crystallin > > found in bull-frog where it acts as 'structural > > protein' to maintain lens transparency. It shows > 55% > > sequence identity with Aldo-keto reductase > superfamily > > which are enzymes. Both proteins have similar > three > > dimensioanl structure and one residue required for > > catalytic activity is absent in rho-crystallin. > > > > Best, > > Shamshad > > > > --- Iddo Friedberg wrote: > > > >>Not to answer your question directly, > >>just to add confusion: > >> > >>How about the same protein which performs > different > >>functions? > >>Crystallins > >>are an example of a protease which, in the eye > lens, > >>serves as a > >>transparent buffer. > >> > >>There are other such "moonlighting proteins" look > >>at: > >> > > > > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12902157&dopt=Abstract > > > >>./I > >> > >>-- > >>Iddo Friedberg, Ph.D. > >>The Burnham Institute > >>10901 N. Torrey Pines Rd. > >>La Jolla, CA 92037, USA > >>Tel: +1 (858) 646 3100 x3516 > >>Fax: +1 (858) 646 3171 > >>http://ffas.ljcrf.edu/~iddo > >> > >>On Fri, 6 Feb 2004, Hongyu Zhang wrote: > >> > >> > >>>Does anyone have examples of two proteins with > >>>90% > >>>identity have differenct functions? I need it as > a > >>>proof to cluster a protein sequence library. > >>> > >>>Thanks! > >>> > >>>Hongyu > >>> > >>>__________________________________ > >>>Do you Yahoo!? > >>>Yahoo! Finance: Get your refund fast by filing > >> > >>online. > >> > >>>http://taxes.yahoo.com/filing.html > >>>_______________________________________________ > >>>BiO_Bulletin_Board maillist - > >> > >>BiO_Bulletin_Board at bioinformatics.org > >> > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > >>_______________________________________________ > >>BiO_Bulletin_Board maillist - > >>BiO_Bulletin_Board at bioinformatics.org > >> > > > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > __________________________________ > > Do you Yahoo!? > > Yahoo! Finance: Get your refund fast by filing > online. > > http://taxes.yahoo.com/filing.html > > _______________________________________________ > > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 713 9930 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________ Do you Yahoo!? Yahoo! Finance: Get your refund fast by filing online. http://taxes.yahoo.com/filing.html From pankaj at nii.res.in Fri Feb 13 06:20:27 2004 From: pankaj at nii.res.in (Pankaj) Date: Fri, 13 Feb 2004 16:50:27 +0530 (IST) Subject: [BiO BB] structure prediction Message-ID: hi all, can someone please suggest some downloadable good threading programs. thanks in advance, Pankaj From Alex.Bossers at wur.nl Fri Feb 13 06:39:36 2004 From: Alex.Bossers at wur.nl (Bossers, Alex) Date: Fri, 13 Feb 2004 12:39:36 +0100 Subject: [BiO BB] structure prediction Message-ID: <839C6D97DA4B564882F385F1DA46742C01C0FC53@slely0004.wurnet.nl> Take al look at the swiss-model homology modelling site. Has good builder/viewer tools incorporated too. http://www.expasy.org/spdbv/mainpage.htm Alex > -----Oorspronkelijk bericht----- > Van: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board- > admin at bioinformatics.org] Namens Pankaj > Verzonden: vrijdag 13 februari 2004 12:20 > Aan: bio_bulletin_board at bioinformatics.org > Onderwerp: [BiO BB] structure prediction > > hi all, > can someone please suggest some downloadable good threading programs. > thanks in advance, > Pankaj > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From penghanchuan at yahoo.com Fri Feb 13 07:22:36 2004 From: penghanchuan at yahoo.com (Hanchuan Peng) Date: Fri, 13 Feb 2004 04:22:36 -0800 (PST) Subject: [BiO BB] structure prediction In-Reply-To: <839C6D97DA4B564882F385F1DA46742C01C0FC53@slely0004.wurnet.nl> Message-ID: <20040213122236.80649.qmail@web41508.mail.yahoo.com> Pls go to Ying Xu's web site at csbl.bmb.uga.edu to take a look. They have a PROSPECT software for protein threading. --Hanchuan --- "Bossers, Alex" wrote: > Take al look at the swiss-model homology modelling site. Has good > builder/viewer tools incorporated too. > http://www.expasy.org/spdbv/mainpage.htm > > Alex > > > > -----Oorspronkelijk bericht----- > > Van: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board- > > admin at bioinformatics.org] Namens Pankaj > > Verzonden: vrijdag 13 februari 2004 12:20 > > Aan: bio_bulletin_board at bioinformatics.org > > Onderwerp: [BiO BB] structure prediction > > > > hi all, > > can someone please suggest some downloadable good threading > programs. > > thanks in advance, > > Pankaj > > _______________________________________________ > > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jeff at bioinformatics.org Sat Feb 14 18:25:41 2004 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sat, 14 Feb 2004 18:25:41 -0500 Subject: [BiO BB] [Fwd: Small Genome Similarity] Message-ID: <402EAE75.3030909@bioinformatics.org> Please CC reply to . Jeff -------------- next part -------------- An embedded message was scrubbed... From: "Tristan Fiedler" Subject: Small Genome Similarity Date: Thu, 12 Feb 2004 19:19:42 -0500 (EST) Size: 2615 URL: From idoerg at burnham.org Sat Feb 14 23:11:02 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat, 14 Feb 2004 20:11:02 -0800 Subject: [BiO BB] [Fwd: Small Genome Similarity] In-Reply-To: <402EAE75.3030909@bioinformatics.org> References: <402EAE75.3030909@bioinformatics.org> Message-ID: <402EF156.40609@burnham.org> Generally, the strategy should be to look for homology in the translated regions, using the protein amino-acid sequence. Protein sequences are much less "noisy" than the DNA sequences coding them, so using a protein sequence your search sensitivity is enhanced. Furthermore, you have better software to match distantly similar sequences using protein sequences, starting at PSI-BLAST and moving up to such stuff as 3D-PSSM, FFAS03, etc. Hope this gets you on the right track. Iddo J.W. Bizzaro wrote: > Please CC reply to . Jeff > > > ------------------------------------------------------------------------ > > Subject: > Small Genome Similarity > From: > "Tristan Fiedler" > Date: > Thu, 12 Feb 2004 19:19:42 -0500 (EST) > To: > Mailman-owner at bioinformatics.org > > > Dear BIO, > > Could you please post the following to the most suitable discussion group > within bioinformatics.org ? Thank you kindly in advance. > > ########################## > I am looking at a novel 2.4 KB viral genome and want to see if anything > homologous is known. > > Have tried blastn,blastx variants but nothing comes up (possibly due to > frame or simply divergence). > > This beastie may replicate in the mitochondria of vertebrates so > translations may need to use mito not nuclear codons. > > Please let me know if you have any suggestions or experience looking at > similar sequences. > > Thank you, > > Tristan > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From val at vtek.com Sun Feb 15 15:48:06 2004 From: val at vtek.com (val) Date: Sun, 15 Feb 2004 15:48:06 -0500 Subject: [BiO BB] [Fwd: Small Genome Similarity] References: <402EAE75.3030909@bioinformatics.org> <402EF156.40609@burnham.org> Message-ID: <1c6301c3f405$0356a650$6400a8c0@vt1000> Yes, seemingly right, but a protein-expression machinery depends as well on local translation env, and may send mixed messages about the DNA features. So, the homologies - yes, but what they indicate? Right? cheers, val ----- Original Message ----- From: "Iddo Friedberg" To: ; Sent: Saturday, February 14, 2004 11:11 PM Subject: Re: [BiO BB] [Fwd: Small Genome Similarity] > > > Generally, the strategy should be to look for homology in the translated > regions, using the protein amino-acid sequence. Protein sequences are > much less "noisy" than the DNA sequences coding them, so using a protein > sequence your search sensitivity is enhanced. > Furthermore, you have better software to match distantly similar > sequences using protein sequences, starting at PSI-BLAST and moving up > to such stuff as 3D-PSSM, FFAS03, etc. > > Hope this gets you on the right track. > > Iddo > > J.W. Bizzaro wrote: > > Please CC reply to . Jeff > > > > > > ------------------------------------------------------------------------ > > > > Subject: > > Small Genome Similarity > > From: > > "Tristan Fiedler" > > Date: > > Thu, 12 Feb 2004 19:19:42 -0500 (EST) > > To: > > Mailman-owner at bioinformatics.org > > > > > > Dear BIO, > > > > Could you please post the following to the most suitable discussion group > > within bioinformatics.org ? Thank you kindly in advance. > > > > ########################## > > I am looking at a novel 2.4 KB viral genome and want to see if anything > > homologous is known. > > > > Have tried blastn,blastx variants but nothing comes up (possibly due to > > frame or simply divergence). > > > > This beastie may replicate in the mitochondria of vertebrates so > > translations may need to use mito not nuclear codons. > > > > Please let me know if you have any suggestions or experience looking at > > similar sequences. > > > > Thank you, > > > > Tristan > > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 713 9930 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From imitra at myezconnect.com Mon Feb 16 02:12:35 2004 From: imitra at myezconnect.com (Indranil Mitra) Date: Mon, 16 Feb 2004 12:42:35 +0530 Subject: [BiO BB] Need Literature on Drug Deliver system In-Reply-To: <20040215170113.065D3D1F18@www.bioinformatics.org> Message-ID: <20040216072908.D8244D1F00@www.bioinformatics.org> Hii, Anybody out there can help me on Drug Delivery related literature/URL etc. Help would be highly appreciated. Best regards, IM -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of bio_bulletin_board-request at bioinformatics.org Sent: Sunday, February 15, 2004 10:31 PM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #637 - 2 msgs From deepan_3356 at yahoo.co.in Mon Feb 16 05:02:05 2004 From: deepan_3356 at yahoo.co.in (=?iso-8859-1?q?deepan=20chakravarthy=20n?=) Date: Mon, 16 Feb 2004 10:02:05 +0000 (GMT) Subject: [BiO BB] gene prediction In-Reply-To: <1c6301c3f405$0356a650$6400a8c0@vt1000> Message-ID: <20040216100205.45974.qmail@web8206.mail.in.yahoo.com> hello, i would like to know some of the softwares that are used for gene prediction for eukaryotes. ===== --------------------------------------------- deepan chakravarthy n 2nd year,(4th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no207, home:04287-241199,04287-244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. Go to: http://in.insurance.yahoo.com/licspecial/index.html From deepan_3356 at yahoo.co.in Mon Feb 16 05:04:12 2004 From: deepan_3356 at yahoo.co.in (=?iso-8859-1?q?deepan=20chakravarthy=20n?=) Date: Mon, 16 Feb 2004 10:04:12 +0000 (GMT) Subject: [BiO BB] bioinformatics algorithms In-Reply-To: <1c6301c3f405$0356a650$6400a8c0@vt1000> Message-ID: <20040216100412.46343.qmail@web8206.mail.in.yahoo.com> hello, i would like to know some websites to learn the basic bioinformatics algorithms. deepan ===== --------------------------------------------- deepan chakravarthy n 2nd year,(4th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no207, home:04287-241199,04287-244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. Go to: http://in.insurance.yahoo.com/licspecial/index.html From B.A.T.Svensson at lumc.nl Mon Feb 16 05:30:13 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Mon, 16 Feb 2004 11:30:13 +0100 Subject: [BiO BB] bioinformatics algorithms Message-ID: http://www.google.nl/search?q=basic+bioinformatics+algorithms&ie=UTF-8&oe=UT F-8&hl=nl&btnG=Google+zoeken&lr== gives +43 thousand hits. -----Original Message----- From: deepan chakravarthy n To: bio_bulletin_board at bioinformatics.org Sent: 2004-02-16 11:04 Subject: [BiO BB] bioinformatics algorithms hello, i would like to know some websites to learn the basic bioinformatics algorithms. deepan ===== --------------------------------------------- deepan chakravarthy n 2nd year,(4th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no207, home:04287-241199,04287-244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. Go to: http://in.insurance.yahoo.com/licspecial/index.html _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From B.A.T.Svensson at lumc.nl Mon Feb 16 05:31:23 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Mon, 16 Feb 2004 11:31:23 +0100 Subject: [BiO BB] gene prediction Message-ID: http://www.google.nl/search?hl=nl&ie=UTF-8&oe=UTF-8&q=gene+prediction+for+eu karyotes&btnG=Google+zoeken&lr= Unfortunately only +16 thousand hits. -----Original Message----- From: deepan chakravarthy n To: bio_bulletin_board at bioinformatics.org Sent: 2004-02-16 11:02 Subject: [BiO BB] gene prediction hello, i would like to know some of the softwares that are used for gene prediction for eukaryotes. ===== --------------------------------------------- deepan chakravarthy n 2nd year,(4th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no207, home:04287-241199,04287-244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. Go to: http://in.insurance.yahoo.com/licspecial/index.html _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Austin.Tanney at arragen.com Mon Feb 16 05:46:23 2004 From: Austin.Tanney at arragen.com (Austin Tanney) Date: Mon, 16 Feb 2004 10:46:23 -0000 Subject: [BiO BB] Need Literature on Drug Deliver system Message-ID: What sort of Drug Delivery??? -----Original Message----- From: Indranil Mitra [mailto:imitra at myezconnect.com] Sent: 16 February 2004 07:13 To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Need Literature on Drug Deliver system Hii, Anybody out there can help me on Drug Delivery related literature/URL etc. Help would be highly appreciated. Best regards, IM -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of bio_bulletin_board-request at bioinformatics.org Sent: Sunday, February 15, 2004 10:31 PM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #637 - 2 msgs _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board This e-mail is from ArraGen Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk at arragen.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraGen Ltd. Registration Number NI 43067 Registered Address : Almac House, Charlestown Road, Craigavon, BT63 5UA Northern Ireland From dmb at mrc-dunn.cam.ac.uk Mon Feb 16 06:21:14 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 16 Feb 2004 11:21:14 +0000 (GMT) Subject: [BiO BB] gene prediction In-Reply-To: Message-ID: perhaps that is the problem? On Mon, 16 Feb 2004, Svensson, B.A.T. (HKG) wrote: > http://www.google.nl/search?hl=nl&ie=UTF-8&oe=UTF-8&q=gene+prediction+for+eu > karyotes&btnG=Google+zoeken&lr= > > Unfortunately only +16 thousand hits. > > -----Original Message----- > From: deepan chakravarthy n > To: bio_bulletin_board at bioinformatics.org > Sent: 2004-02-16 11:02 > Subject: [BiO BB] gene prediction > > hello, > i would like to know some of the softwares that > are > used for gene prediction for eukaryotes. > > > ===== > --------------------------------------------- > deepan chakravarthy n > 2nd year,(4th sem), > b.tech(biotech), > center for biotechnology, > anna university , > chennai. > ph no: > hostel:044-22354862,room no207, > home:04287-241199,04287-244399, > address: > ac tech hostel (jh 207), > anna university, > chennai-25. > > ________________________________________________________________________ > Yahoo! India Insurance Special: Be informed on the best policies, > services, tools and more. > Go to: http://in.insurance.yahoo.com/licspecial/index.html > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From letondal at pasteur.fr Mon Feb 16 06:31:40 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Mon, 16 Feb 2004 12:31:40 +0100 Subject: [BiO BB] bioinformatics algorithms In-Reply-To: Your message of "Mon, 16 Feb 2004 11:30:13 +0100." Message-ID: <200402161131.i1GBVe4d368796@electre.pasteur.fr> Hi, You can try: http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?english=1&query=algorithm "Svensson, B.A.T. (HKG)" wrote: > http://www.google.nl/search?q=basic+bioinformatics+algorithms&ie=UTF-8&oe=UT > F-8&hl=nl&btnG=Google+zoeken&lr== > > gives +43 thousand hits. > > -----Original Message----- > From: deepan chakravarthy n > To: bio_bulletin_board at bioinformatics.org > Sent: 2004-02-16 11:04 > Subject: [BiO BB] bioinformatics algorithms > > hello, > i would like to know some websites to learn the > basic bioinformatics algorithms. > deepan > -- Catherine Letondal -- Pasteur Institute Computing Center From prathibha_562 at yahoo.co.in Mon Feb 16 07:06:10 2004 From: prathibha_562 at yahoo.co.in (=?iso-8859-1?q?prathibha=20bharathi?=) Date: Mon, 16 Feb 2004 12:06:10 +0000 (GMT) Subject: [BiO BB] bioinformatics algorithms In-Reply-To: <20040216100412.46343.qmail@web8206.mail.in.yahoo.com> Message-ID: <20040216120610.86151.qmail@web8201.mail.in.yahoo.com> Hello... There is one book(very good) "BIOINFORMATICS" by Prof:David Mount .Try this and visit it's companion website http://www.bioinformaticsonline.org one imp thing here is you must have the access code to get registered, to read the contents of the website.You can find the access code on the inside front cover of the book. hope u can find some stuff (which u want) there. This may help u ,if u are a fresher to this field;( I don't about Gurus of this field) bye Prathibha, B-tech (final year), Sree Vidyaniketan Engineering college. Andhra Pradesh, India. deepan chakravarthy n wrote: hello, i would like to know some websites to learn the basic bioinformatics algorithms. deepan ===== --------------------------------------------- deepan chakravarthy n 2nd year,(4th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no207, home:04287-241199,04287-244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. Go to: http://in.insurance.yahoo.com/licspecial/index.html _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. -------------- next part -------------- An HTML attachment was scrubbed... URL: From imitra at myezconnect.com Mon Feb 16 23:19:43 2004 From: imitra at myezconnect.com (Indranil Mitra) Date: Tue, 17 Feb 2004 09:49:43 +0530 Subject: [BiO BB] Drug Delivery In-Reply-To: <20040216170119.E6A28D1EFB@www.bioinformatics.org> Message-ID: <20040217042552.B10C2D1F00@www.bioinformatics.org> I need the information on drug delivery mechanism for customized drugs. Best Regards, IM -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of bio_bulletin_board-request at bioinformatics.org Sent: Monday, February 16, 2004 10:31 PM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #638 - 10 msgs When replying, PLEASE edit your Subject line so it is more specific than "Re: BiO_Bulletin_Board digest, Vol..." And, PLEASE delete any unrelated text from the body. Today's Topics: 1. Re: [Fwd: Small Genome Similarity] (val) 2. Need Literature on Drug Deliver system (Indranil Mitra) 3. gene prediction (=?iso-8859-1?q?deepan=20chakravarthy=20n?=) 4. bioinformatics algorithms (=?iso-8859-1?q?deepan=20chakravarthy=20n?=) 5. RE: bioinformatics algorithms (Svensson, B.A.T. (HKG)) 6. RE: gene prediction (Svensson, B.A.T. (HKG)) 7. RE: Need Literature on Drug Deliver system (Austin Tanney) 8. RE: gene prediction (Dan Bolser) 9. Re: bioinformatics algorithms (Catherine Letondal) 10. Re: bioinformatics algorithms (=?iso-8859-1?q?prathibha=20bharathi?=) --__--__-- Message: 1 From: "val" To: Subject: Re: [BiO BB] [Fwd: Small Genome Similarity] Date: Sun, 15 Feb 2004 15:48:06 -0500 Reply-To: bio_bulletin_board at bioinformatics.org Yes, seemingly right, but a protein-expression machinery depends as well on local translation env, and may send mixed messages about the DNA features. So, the homologies - yes, but what they indicate? Right? cheers, val ----- Original Message ----- From: "Iddo Friedberg" To: ; Sent: Saturday, February 14, 2004 11:11 PM Subject: Re: [BiO BB] [Fwd: Small Genome Similarity] > > > Generally, the strategy should be to look for homology in the translated > regions, using the protein amino-acid sequence. Protein sequences are > much less "noisy" than the DNA sequences coding them, so using a protein > sequence your search sensitivity is enhanced. > Furthermore, you have better software to match distantly similar > sequences using protein sequences, starting at PSI-BLAST and moving up > to such stuff as 3D-PSSM, FFAS03, etc. > > Hope this gets you on the right track. > > Iddo > > J.W. Bizzaro wrote: > > Please CC reply to . Jeff > > > > > > ------------------------------------------------------------------------ > > > > Subject: > > Small Genome Similarity > > From: > > "Tristan Fiedler" > > Date: > > Thu, 12 Feb 2004 19:19:42 -0500 (EST) > > To: > > Mailman-owner at bioinformatics.org > > > > > > Dear BIO, > > > > Could you please post the following to the most suitable discussion group > > within bioinformatics.org ? Thank you kindly in advance. > > > > ########################## > > I am looking at a novel 2.4 KB viral genome and want to see if anything > > homologous is known. > > > > Have tried blastn,blastx variants but nothing comes up (possibly due to > > frame or simply divergence). > > > > This beastie may replicate in the mitochondria of vertebrates so > > translations may need to use mito not nuclear codons. > > > > Please let me know if you have any suggestions or experience looking at > > similar sequences. > > > > Thank you, > > > > Tristan > > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 713 9930 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > --__--__-- Message: 2 From: "Indranil Mitra" To: Date: Mon, 16 Feb 2004 12:42:35 +0530 Organization: MEC Technologies Subject: [BiO BB] Need Literature on Drug Deliver system Reply-To: bio_bulletin_board at bioinformatics.org Hii, Anybody out there can help me on Drug Delivery related literature/URL etc. Help would be highly appreciated. Best regards, IM -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of bio_bulletin_board-request at bioinformatics.org Sent: Sunday, February 15, 2004 10:31 PM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #637 - 2 msgs --__--__-- Message: 3 Date: Mon, 16 Feb 2004 10:02:05 +0000 (GMT) From: =?iso-8859-1?q?deepan=20chakravarthy=20n?= To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] gene prediction Reply-To: bio_bulletin_board at bioinformatics.org hello, i would like to know some of the softwares that are used for gene prediction for eukaryotes. ===== --------------------------------------------- deepan chakravarthy n 2nd year,(4th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no207, home:04287-241199,04287-244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. Go to: http://in.insurance.yahoo.com/licspecial/index.html --__--__-- Message: 4 Date: Mon, 16 Feb 2004 10:04:12 +0000 (GMT) From: =?iso-8859-1?q?deepan=20chakravarthy=20n?= To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] bioinformatics algorithms Reply-To: bio_bulletin_board at bioinformatics.org hello, i would like to know some websites to learn the basic bioinformatics algorithms. deepan ===== --------------------------------------------- deepan chakravarthy n 2nd year,(4th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no207, home:04287-241199,04287-244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. Go to: http://in.insurance.yahoo.com/licspecial/index.html --__--__-- Message: 5 From: "Svensson, B.A.T. (HKG)" To: "'bio_bulletin_board at bioinformatics.org '" Subject: RE: [BiO BB] bioinformatics algorithms Date: Mon, 16 Feb 2004 11:30:13 +0100 Reply-To: bio_bulletin_board at bioinformatics.org http://www.google.nl/search?q=basic+bioinformatics+algorithms&ie=UTF-8&oe=UT F-8&hl=nl&btnG=Google+zoeken&lr== gives +43 thousand hits. -----Original Message----- From: deepan chakravarthy n To: bio_bulletin_board at bioinformatics.org Sent: 2004-02-16 11:04 Subject: [BiO BB] bioinformatics algorithms hello, i would like to know some websites to learn the basic bioinformatics algorithms. deepan ===== --------------------------------------------- deepan chakravarthy n 2nd year,(4th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no207, home:04287-241199,04287-244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. Go to: http://in.insurance.yahoo.com/licspecial/index.html _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --__--__-- Message: 6 From: "Svensson, B.A.T. (HKG)" To: "'bio_bulletin_board at bioinformatics.org '" Subject: RE: [BiO BB] gene prediction Date: Mon, 16 Feb 2004 11:31:23 +0100 Reply-To: bio_bulletin_board at bioinformatics.org http://www.google.nl/search?hl=nl&ie=UTF-8&oe=UTF-8&q=gene+prediction+for+eu karyotes&btnG=Google+zoeken&lr= Unfortunately only +16 thousand hits. -----Original Message----- From: deepan chakravarthy n To: bio_bulletin_board at bioinformatics.org Sent: 2004-02-16 11:02 Subject: [BiO BB] gene prediction hello, i would like to know some of the softwares that are used for gene prediction for eukaryotes. ===== --------------------------------------------- deepan chakravarthy n 2nd year,(4th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no207, home:04287-241199,04287-244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. Go to: http://in.insurance.yahoo.com/licspecial/index.html _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --__--__-- Message: 7 Subject: RE: [BiO BB] Need Literature on Drug Deliver system Date: Mon, 16 Feb 2004 10:46:23 -0000 From: "Austin Tanney" To: Reply-To: bio_bulletin_board at bioinformatics.org What sort of Drug Delivery??? -----Original Message----- From: Indranil Mitra [mailto:imitra at myezconnect.com] Sent: 16 February 2004 07:13 To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Need Literature on Drug Deliver system Hii, Anybody out there can help me on Drug Delivery related literature/URL = etc. Help would be highly appreciated. Best regards, IM -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of bio_bulletin_board-request at bioinformatics.org Sent: Sunday, February 15, 2004 10:31 PM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #637 - 2 msgs _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board This e-mail is from ArraGen Ltd The e-mail and any files transmitted with it are confidential and = privileged and intended solely for the use of the individual or entity = to whom they are addressed.=20 Any unauthorised direct or indirect dissemination, distribution or = copying of this message and any attachments is strictly prohibited.=20 If you have received the e-mail in error please notify = helpdesk at arragen.com or telephone +44 28 38 363841 and delete the e-mail = from your system. E-mail and other communications sent to this company may be reviewed or = read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and = any attachments are free from any virus, you should, in keeping with = good practice, ensure that they are actually virus free. ArraGen Ltd. Registration Number NI 43067 Registered Address : Almac House, Charlestown Road, Craigavon, BT63 5UA = Northern Ireland --__--__-- Message: 8 Date: Mon, 16 Feb 2004 11:21:14 +0000 (GMT) From: Dan Bolser To: "'bio_bulletin_board at bioinformatics.org '" Subject: RE: [BiO BB] gene prediction Reply-To: bio_bulletin_board at bioinformatics.org perhaps that is the problem? On Mon, 16 Feb 2004, Svensson, B.A.T. (HKG) wrote: > http://www.google.nl/search?hl=nl&ie=UTF-8&oe=UTF-8&q=gene+prediction+for+eu > karyotes&btnG=Google+zoeken&lr= > > Unfortunately only +16 thousand hits. > > -----Original Message----- > From: deepan chakravarthy n > To: bio_bulletin_board at bioinformatics.org > Sent: 2004-02-16 11:02 > Subject: [BiO BB] gene prediction > > hello, > i would like to know some of the softwares that > are > used for gene prediction for eukaryotes. > > > ===== > --------------------------------------------- > deepan chakravarthy n > 2nd year,(4th sem), > b.tech(biotech), > center for biotechnology, > anna university , > chennai. > ph no: > hostel:044-22354862,room no207, > home:04287-241199,04287-244399, > address: > ac tech hostel (jh 207), > anna university, > chennai-25. > > ________________________________________________________________________ > Yahoo! India Insurance Special: Be informed on the best policies, > services, tools and more. > Go to: http://in.insurance.yahoo.com/licspecial/index.html > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > --__--__-- Message: 9 From: Catherine Letondal To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] bioinformatics algorithms Date: Mon, 16 Feb 2004 12:31:40 +0100 Reply-To: bio_bulletin_board at bioinformatics.org Hi, You can try: http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?english=1&query=algorithm "Svensson, B.A.T. (HKG)" wrote: > http://www.google.nl/search?q=basic+bioinformatics+algorithms&ie=UTF-8&oe=UT > F-8&hl=nl&btnG=Google+zoeken&lr== > > gives +43 thousand hits. > > -----Original Message----- > From: deepan chakravarthy n > To: bio_bulletin_board at bioinformatics.org > Sent: 2004-02-16 11:04 > Subject: [BiO BB] bioinformatics algorithms > > hello, > i would like to know some websites to learn the > basic bioinformatics algorithms. > deepan > -- Catherine Letondal -- Pasteur Institute Computing Center --__--__-- Message: 10 Date: Mon, 16 Feb 2004 12:06:10 +0000 (GMT) From: =?iso-8859-1?q?prathibha=20bharathi?= Subject: Re: [BiO BB] bioinformatics algorithms To: bio_bulletin_board at bioinformatics.org Reply-To: bio_bulletin_board at bioinformatics.org --0-1554242831-1076933170=:84683 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello... There is one book(very good) "BIOINFORMATICS" by Prof:David Mount .Try this and visit it's companion website http://www.bioinformaticsonline.org one imp thing here is you must have the access code to get registered, to read the contents of the website.You can find the access code on the inside front cover of the book. hope u can find some stuff (which u want) there. This may help u ,if u are a fresher to this field;( I don't about Gurus of this field) bye Prathibha, B-tech (final year), Sree Vidyaniketan Engineering college. Andhra Pradesh, India. deepan chakravarthy n wrote: hello, i would like to know some websites to learn the basic bioinformatics algorithms. deepan ===== --------------------------------------------- deepan chakravarthy n 2nd year,(4th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: hostel:044-22354862,room no207, home:04287-241199,04287-244399, address: ac tech hostel (jh 207), anna university, chennai-25. ________________________________________________________________________ Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. Go to: http://in.insurance.yahoo.com/licspecial/index.html _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. --0-1554242831-1076933170=:84683 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hello...
      There is one book(very good) "BIOINFORMATICS" by Prof:David Mount .Try this and visit it's companion website http://www.bioinformaticsonline.o rg
one imp thing here is you must have the access code to get registered, to read the contents of the website.You can find the access code on the inside front cover of the book.
             ;            &nb sp;       hope u can find some stuff (which u want) there.
 This may help u ,if u are a fresher to this field;( I don't about Gurus of this field)
             ;            &nb sp;            & nbsp;             ;        bye
             ;            &nb sp;            & nbsp;             ;     Prathibha,
             ;            &nb sp;            & nbsp;         B-tech (fina l year),
             ;            &nb sp;            & nbsp;         Sree Vidyaniketan Engineering college.
             ;            &nb sp;            & nbsp;         Andhra Pradesh,
             ;            &nb sp;            & nbsp;          India.
 
             ;            &nb sp;            & nbsp;         
deepan chakravarthy n <deepan_3356 at yahoo.co.in> wrote:
hello,
i would like to know some websites to learn the
basic bioinformatics algorithms.
deepan

=====
-------------------------------------- -------
deepan chakravarthy n
2nd year,(4th sem),
b.tech(biotech),
center for biotechnology,
anna university ,
chennai.
ph no:
hostel:044-22354862,room no207,
home:04287-241199,04287-244399,
address:
ac tech hostel (jh 207),
anna university,
chennai-25.

__________________________________________ ______________________________
Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more.
Go to: http://in.insurance.yahoo.com/licspecial/index.html
_____________________ __________________________
BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
https://bioinformatics.org/mailman/ listinfo/bio_bulletin_board

Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. --0-1554242831-1076933170=:84683-- --__--__-- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest From bioburri at yahoo.de Tue Feb 17 09:25:09 2004 From: bioburri at yahoo.de (=?iso-8859-1?q?Raghu=20burri?=) Date: Tue, 17 Feb 2004 15:25:09 +0100 (CET) Subject: [BiO BB] Need Literature on Drug Deliver system Message-ID: <20040217142509.12970.qmail@web40504.mail.yahoo.com> If U want information on Drug Discovery, join in Cheminformatics yahoo groups. http://groups.yahoo.com/group/cheminformatics/ The Web advertisement for CHEMINFORMATICS GROUP describes the field thus: "the combination of chemical synthesis, biological screening, and data-mining approaches used to guide drug discovery and development" but this, again, sounds more like a field being identified by some of its most popular (and lucrative) activities, rather than by including all the diverse studies that come under its general heading. The story of one of the most successful drugs of all time, penicillin, seems bizarre, but the way we discover and develop drugs even now has similarities, being the result of chance, observation and a lot of slow, intensive chemistry. Until recently, drug design always seemed doomed to continue to be a labour-intensive, trial-and-error process. The possibility of using information technology, to plan intelligently and to automate processes related to the chemical synthesis of possible therapeutic compounds is very exciting for chemists and biochemists. The rewards for bringing a drug to market more rapidly are huge, so naturally this is what a lot of cheminformatics works is about. Here is a group with a young people who are interesting discussions of the term "cheminformatics", what it means, whether or not it exists as a distinct discipline, and even whether it should be replaced by "chemoinformatics". The aim of this group is to share there ideas and relate experimental observations or exprience in the field of Cheminformatics. Bye RB Mit sch?nen Gr??en von Yahoo! Mail - http://mail.yahoo.de From mgollery at unr.edu Wed Feb 18 19:45:52 2004 From: mgollery at unr.edu (Martin Gollery) Date: Wed, 18 Feb 2004 16:45:52 -0800 Subject: [BiO BB] [Fwd: Small Genome Similarity] In-Reply-To: <402EAE75.3030909@bioinformatics.org> References: <402EAE75.3030909@bioinformatics.org> Message-ID: <1077151552.4034074051e07@webmail.unr.edu> Tristan, Try going to Blosum30 for the matrix, and lower the open and extend gap penalties, and lower the reporting threshold. Use the mito codons. If you still don't get hits, switch from BLAST to Smith-Waterman, or use Interproscan to compare it to several signature databases. Marty Quoting "J.W. Bizzaro" : >I am looking at a novel 2.4 KB viral genome and want to see if anything >homologous is known. > >Have tried blastn,blastx variants but nothing comes up (possibly due to >frame or simply divergence). > >This beastie may replicate in the mitochondria of vertebrates so >translations may need to use mito not nuclear codons. > >Please let me know if you have any suggestions or experience looking at >similar sequences. > >Thank you, > >Tristan Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From dmb at mrc-dunn.cam.ac.uk Thu Feb 19 14:31:23 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 19 Feb 2004 19:31:23 +0000 (GMT) Subject: [BiO BB] CD-HIT project started at Bioinformatics.Org ! Message-ID: Weizhong Li has moved his popular cd-hit software to bioinformatics.org and created a new open source project! cd-hit is used in a wide variety of applications, helping many people quickly and efficiently create non-redundant sequence databases at high sequence identity. Now the software is *open* for community development - which means you too can help improve this already excellent package! We are looking for developers and researchers of all experience levels to... * Make cd-hit compatible with existing sequence IO libraries, to expand the range of allowed input formats. * Develop a range of useful output formats, including XML. * Package cd-hit with gnu configure utilities to expand the range of platforms for which cd-hit can be reliably used. * Research the all important sequence clustering benchmark 'sub project' of cd-hit, working to develop rigorous measures of sensitivity, selectivity and optimisation for a range of clustering tools and parameters. * Begin to KO the few existing bugs in the cd-hit bug list. Also, if you use cd-hit, we would like to know! From rong at bu.edu Thu Feb 19 21:07:54 2004 From: rong at bu.edu (Rong Chen) Date: Thu, 19 Feb 2004 21:07:54 -0500 (EST) Subject: [BiO BB] Software to identify ligand in electron density map. In-Reply-To: <1058298374.3556.1.camel@squash.scalableinformatics.com> Message-ID: Hi, friends, I am looking for a software to identify ligands in electron density map. We are solving protein structures using X-ray in high throughput. Sometimes, ligands gets into the crystal in the pipeline, as shown in the electron density map. Is there any software to identify the ligand according to the electron density map? I know that X-Ligand can do it, but it is very expensive. Does anyone know any academic software for this purpose? Thank you very much for your help. Best regards, Rong From hk_soni2003 at indiatimes.com Fri Feb 20 06:44:48 2004 From: hk_soni2003 at indiatimes.com (hk_soni2003) Date: Fri, 20 Feb 2004 17:14:48 +0530 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #640 - 1 msg Message-ID: <200402201124.QAA23042@WS0005.indiatimes.com> bio_bulletin_board at bioinformatics.org wrote: When replying, PLEASE edit your Subject line so it is more specific than "Re: BiO_Bulletin_Board digest, Vol..." And, PLEASE delete any unrelated text from the body. Today's Topics: 1. Re: [Fwd: Small Genome Similarity] (Martin Gollery) --__--__-- Message: 1 Date: Wed, 18 Feb 2004 16:45:52 -0800 From: Martin Gollery To: bio_bulletin_board at bioinformatics.org Cc: t.fiedler at umiami.edu Subject: Re: [BiO BB] [Fwd: Small Genome Similarity] Reply-To: bio_bulletin_board at bioinformatics.org Tristan, Try going to Blosum30 for the matrix, and lower the open and extend gap penalties, and lower the reporting threshold. Use the mito codons. If you still don't get hits, switch from BLAST to Smith-Waterman, or use Interproscan to compare it to several signature databases. Marty Quoting "J.W. Bizzaro" : >I am looking at a novel 2.4 KB viral genome and want to see if anything >homologous is known. > >Have tried blastn,blastx variants but nothing comes up (possibly due to >frame or simply divergence). > >This beastie may replicate in the mitochondria of vertebrates so >translations may need to use mito not nuclear codons. > >Please let me know if you have any suggestions or experience looking at >similar sequences. > >Thank you, > >Tristan Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu --__--__-- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest Indiatimes Email now powered by APIC Advantage. Help! HelpClick onthe image to chat with me -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanielager at fastmail.ca Mon Feb 23 04:47:16 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 23 Feb 2004 09:47:16 +0000 (UTC) Subject: [BiO BB] Seqio and fmtseq Message-ID: <20040223094716.969FF8658EC@mail.interchange.ca> Hi, I have problems to compile the Seqio library and specifically the fmtseq sequence format conversion program, on Linux. It seems as if line 150 in seqio.c and line 40 in fmtseq.c (extern char *sys_errlist[]) is in conflict with stdio.h (gcc version 3.2.2). I've tried to comment out these two lines, and then it compiles, but when I try to run fmtseq it crashes with "Segmentation fault". Does anyone know how to modify seqio.c and fmtseq.c, so they can be compiled on Linux? Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From landman at scalableinformatics.com Mon Feb 23 07:00:05 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Mon, 23 Feb 2004 07:00:05 -0500 Subject: [BiO BB] Seqio and fmtseq In-Reply-To: <20040223094716.969FF8658EC@mail.interchange.ca> References: <20040223094716.969FF8658EC@mail.interchange.ca> Message-ID: <1077537604.3932.2.camel@protein.scalableinformatics.com> Did you add a -D__unix to the compile line? [landman at protein.scalableinformatics.com:~/seqio-1.2.2] 120 >./fmtseq Input: *none* (format: *auto*) Output: *stdout* (format: *none*) Deflts: -verbose -gapin=- -gapout=- -bigalign Options: -all Warning: An input file and output format must be specified. Commands (-option - set option, -no... - unset option, ? -help - list options, -r -run - execute, -q -quit - exit program, other - set input file) Enter: I can package up this directory and build an RPM out of it if there is interest. Joe On Mon, 2004-02-23 at 04:47, Stefanie Lager wrote: > Hi, > > I have problems to compile the Seqio library and specifically the fmtseq > sequence format conversion program, on Linux. It seems as if line 150 in > seqio.c and line 40 in fmtseq.c (extern char *sys_errlist[]) is in > conflict with stdio.h (gcc version 3.2.2). I've tried to comment out > these two lines, and then it compiles, but when I try to run fmtseq it > crashes with "Segmentation fault". Does anyone know how to modify > seqio.c and fmtseq.c, so they can be compiled on Linux? > > Stefanie > _________________________________________________________________ > http://fastmail.ca/ - Fast Secure Web Email for Canadians > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Joe Landman From stefanielager at fastmail.ca Mon Feb 23 07:36:32 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 23 Feb 2004 12:36:32 +0000 (UTC) Subject: [BiO BB] Seqio and fmtseq In-Reply-To: <1077537604.3932.2.camel@protein.scalableinformatics.com> Message-ID: <20040223123633.F2922861D47@mail.interchange.ca> Thank you, I really don't know much about compilation of c programs, so I don't know what "-D__unix" means, and how it should be added? Stefanie > Did you add a > > -D__unix > > to the compile line? > > [landman at protein.scalableinformatics.com:~/seqio-1.2.2] > 120 >./fmtseq > > Input: *none* (format: *auto*) > Output: *stdout* (format: *none*) > Deflts: -verbose -gapin=- -gapout=- -bigalign > Options: -all > > Warning: An input file and output format must be specified. > > Commands (-option - set option, -no... - unset option, ? -help - list > options, > -r -run - execute, -q -quit - exit program, other - set input > file) > Enter: > > I can package up this directory and build an RPM out of it if there is > interest. > > Joe > > On Mon, 2004-02-23 at 04:47, Stefanie Lager wrote: >> Hi, >> >> I have problems to compile the Seqio library and specifically the >> fmtseq sequence format conversion program, on Linux. It seems as if >> line 150 in seqio.c and line 40 in fmtseq.c (extern char >> *sys_errlist[]) is in conflict with stdio.h (gcc version 3.2.2). I've >> tried to comment out these two lines, and then it compiles, but when >> I try to run fmtseq it crashes with "Segmentation fault". Does anyone >> know how to modify seqio.c and fmtseq.c, so they can be compiled on >> Linux? >> >> Stefanie >> _________________________________________________________________ >> http://fastmail.ca/ - Fast Secure Web Email for Canadians >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- > Joe Landman > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From landman at scalableinformatics.com Mon Feb 23 07:52:03 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Mon, 23 Feb 2004 07:52:03 -0500 Subject: [BiO BB] Seqio and fmtseq In-Reply-To: <20040223123633.F2922861D47@mail.interchange.ca> References: <20040223123633.F2922861D47@mail.interchange.ca> Message-ID: <1077540722.3932.11.camel@protein.scalableinformatics.com> On Mon, 2004-02-23 at 07:36, Stefanie Lager wrote: > Thank you, > > I really don't know much about compilation of c programs, so I don't > know what "-D__unix" means, and how it should be added? Ok, edit the "Makefile" and make the CFLAGS line look like this: CFLAGS= -g -O2 -Wall -Wshadow -D__unix Then from the command prompt rm -f *.o make You will get lots of warnings, but it should work. Joe > > Stefanie > > > Did you add a > > > > -D__unix > > > > to the compile line? > > > > [landman at protein.scalableinformatics.com:~/seqio-1.2.2] > > 120 >./fmtseq > > > > Input: *none* (format: *auto*) > > Output: *stdout* (format: *none*) > > Deflts: -verbose -gapin=- -gapout=- -bigalign > > Options: -all > > > > Warning: An input file and output format must be specified. > > > > Commands (-option - set option, -no... - unset option, ? -help - list > > options, > > -r -run - execute, -q -quit - exit program, other - set input > > file) > > Enter: > > > > I can package up this directory and build an RPM out of it if there is > > interest. > > > > Joe > > > > On Mon, 2004-02-23 at 04:47, Stefanie Lager wrote: > >> Hi, > >> > >> I have problems to compile the Seqio library and specifically the > >> fmtseq sequence format conversion program, on Linux. It seems as if > >> line 150 in seqio.c and line 40 in fmtseq.c (extern char > >> *sys_errlist[]) is in conflict with stdio.h (gcc version 3.2.2). I've > >> tried to comment out these two lines, and then it compiles, but when > >> I try to run fmtseq it crashes with "Segmentation fault". Does anyone > >> know how to modify seqio.c and fmtseq.c, so they can be compiled on > >> Linux? > >> > >> Stefanie > >> _________________________________________________________________ > >> http://fastmail.ca/ - Fast Secure Web Email for Canadians > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- > > Joe Landman > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _________________________________________________________________ > http://fastmail.ca/ - Fast Secure Web Email for Canadians > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From stefanielager at fastmail.ca Mon Feb 23 08:25:42 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 23 Feb 2004 13:25:42 +0000 (UTC) Subject: [BiO BB] Seqio and fmtseq In-Reply-To: <1077540722.3932.11.camel@protein.scalableinformatics.com> Message-ID: <20040223135657.F1BF586123D@mail.interchange.ca> I've tried adding -D__unix to the Makefile, but I still get the "conflicting types for sys_errlist" for: grepseq.c:21 seqio.c:150 fmtseq.c:40 No executables made, so I really don't see the difference? Stefanie > > Ok, edit the "Makefile" and make the CFLAGS line look like this: > > CFLAGS= -g -O2 -Wall -Wshadow -D__unix > > Then from the command prompt > > rm -f *.o > make > > You will get lots of warnings, but it should work. > > Joe > >> >> Stefanie >> >>> Did you add a >>> >>> -D__unix >>> >>> to the compile line? >>> >>> [landman at protein.scalableinformatics.com:~/seqio-1.2.2] >>> 120 >./fmtseq >>> >>> Input: *none* (format: *auto*) >>> Output: *stdout* (format: *none*) >>> Deflts: -verbose -gapin=- -gapout=- -bigalign >>> Options: -all >>> >>> Warning: An input file and output format must be specified. >>> >>> Commands (-option - set option, -no... - unset option, ? -help - >>> list options, >>> -r -run - execute, -q -quit - exit program, other - set input >>> file) >>> Enter: >>> >>> I can package up this directory and build an RPM out of it if there >>> is interest. >>> >>> Joe >>> >>> On Mon, 2004-02-23 at 04:47, Stefanie Lager wrote: >>>> Hi, >>>> >>>> I have problems to compile the Seqio library and specifically the >>>> fmtseq sequence format conversion program, on Linux. It seems as if >>>> line 150 in seqio.c and line 40 in fmtseq.c (extern char >>>> *sys_errlist[]) is in conflict with stdio.h (gcc version 3.2.2). >>>> I've tried to comment out these two lines, and then it compiles, >>>> but when I try to run fmtseq it crashes with "Segmentation fault". >>>> Does anyone know how to modify seqio.c and fmtseq.c, so they can be >>>> compiled on Linux? >>>> >>>> Stefanie >>>> _________________________________________________________________ >>>> http://fastmail.ca/ - Fast Secure Web Email for Canadians >>>> _______________________________________________ >>>> BiO_Bulletin_Board maillist - >>>> BiO_Bulletin_Board at bioinformatics.org >>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >>> -- >>> Joe Landman >>> >>> _______________________________________________ >>> BiO_Bulletin_Board maillist - >>> BiO_Bulletin_Board at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> _________________________________________________________________ >> http://fastmail.ca/ - Fast Secure Web Email for Canadians >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From hjm at tacgi.com Mon Feb 23 13:16:41 2004 From: hjm at tacgi.com (Harry J Mangalam) Date: Mon, 23 Feb 2004 10:16:41 -0800 Subject: [BiO BB] Seqio and fmtseq In-Reply-To: <200402230808.25178.hjm@tacgi.com> References: <20040223094716.969FF8658EC@mail.interchange.ca> <200402230808.25178.hjm@tacgi.com> Message-ID: <200402231016.41164.hjm@tacgi.com> My apologies, I mistakenly sent a large src code file to the list, when I meant to send it only to the person having the problem and mailman alerted me to it. List maintainer, please refuse the file and delete it. Sorry again - Harry On Monday 23 February 2004 08:08 am, Harry J Mangalam wrote: > HI Stephanie, > > I use seqio in tacg and ran across these as well and I think I fixed them a > while ago. Mine compiles fine, so just replace yours with mine and see > what happens. > > You may have to add these line to the top of the grepseq program as well to > get it to see it correctly: > > extern char *sys_errlist[]; > extern const char *const sys_errlist[]; > > Do beware that while seqio is a really useful lib and grepseq is a good > program for a demo of Udi Manber's agrep code applied to molbio, the output > of it is next to useless for real work because of some odd limitations that > Jim Knight coded into it. > > Harry [etc] -- Cheers, Harry Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com <> From jeff at bioinformatics.org Tue Feb 24 09:42:21 2004 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 24 Feb 2004 09:42:21 -0500 Subject: [BiO BB] Reminder: Early Bird and BiO member discount deadline for the 4thAM is this Friday Message-ID: <403B62CD.6040500@bioinformatics.org> The 4th Annual Meeting of the Bioinformatics Organization, Inc. (Bioinformatics.Org) will be held March 30 - April 1, 2004 at the Bio-IT World Conference + Expo, at the Hynes Convention Center, Boston, Massachusetts, USA. This is our East-Coast event for the spring, and all are invited to attend. Bio-IT World is offering a registration discount for all members of Bioinformatics.Org. Those who register online by February 27, 2004 will receive a 25% discount off all early bird conference packages to the Bio-IT World Conference + Expo: http://www.bio-itworldexpo.com/ IMPORTANT: To receive the 25% discount, please register online by February 27, 2004 with the exclusive Bioinformatics.Org member PRIORITY CODE: BTA2 Our participation includes the co-organization of the Bioclusters Workshop (March 30, all day), presentation of the 2004 Benjamin Franklin Award in Bioinformatics (March 31, 8:30 AM), and a reception where new features and resources will be announced (date/time TBA). More information on the event has been provided by Bio-IT World below: For the 3rd consecutive year, Bio-IT World Conference + Expo(tm) returns to Boston's Hynes Convention Center, March 30 - April 1, 2004 and online registration is now open. By attending the conference program, you will learn even more on the technological advances in drug discovery and delivery than ever before. You'll take back valuable tips on how to make your job easier and your company more profitable. Read on to see how... Collaboration with several leading industry partners such as Bio-IT World magazine, Thomson CenterWatch, Medical Records Institute (MRI), Bioinformatics.Org, Ernst & Young, IDC and IDG Ventures will provide you with educational content found at no other event. HERE IS WHAT YOU HAVE TO LOOK FORWARD TO! ============================================================== IN-DEPTH WORKSHOPS Offering you the opportunity to quickly become more knowledgeable on a specialized topic such as Bioclusters, Life Science Identifiers (LSID), Document Management and Regulatory Compliance, Systems Biology and Conducting a BioLaw and Business Strategic Audit (tm). http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10139&p_navID=18 THE DRUGGABLE GENOME This two day track will help you identify promising new drug targets and prioritize leads, diagnose high-risk individuals and populations, and apply an army of in silico and laboratory tools to harness this knowledge to rationally design drugs and expedite their development all through the use of technology. http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10014&p_navID=18#track1 INFORMATICS & IT INFRASTRUCTURE By attending these sessions you will be able to combat the new challenges that are associated with data management and computational workflows with enabling technologies, both software and hardware. Due to the critical nature of these advances in supercomputing and informatics, you need to stay up-to-date for the success of your research and development initiatives. Sponsored by Netezza http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10014&p_navID=18#track2 E-CLINICAL TRIALS RESEARCH You may be currently facing rising costs, intense competition, regulatory pressures and shortages of qualified professionals and patients. Bio-IT World Conference will provide you with the essential information on ways to streamline performance, increase efficiency, coordinate patient recruitment and record-keeping, and improve regulatory compliance. Co-Chaired by Thomson CenterWatch http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10014&p_navID=18#track3 CO-LOCATED HEALTH-IT WORLD CONFERENCE Join hospitals and clinical centers nationwide who have been implementing mobile devices, electronic medical records and computer physician order entry technologies and more which have made significant impacts on the doctor/patient relationship, efficiencies, return on investments and patient safety issues. Co-Chaired by Medical Records Institute and Health-IT World. http://www.health-itworldexpo.com/healthworldexpo/V40/index.cvn?id=10180&p_navID=18 KEYNOTES http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10146&p_navID=115 ============================================================== * Dr. George Poste, Healthcare Networks * Dr. Susan L. Linquist, Whitehead Institute for Biomedical Research * Michael C. Ruettgers, EMC * Steven H. Holtzman, Infinity Pharmaceuticals * Dr. Peter L. Elkin, Mayo Medical School * Dr. John Parrish, The Center for the Integration of Medicine and Innovative Technology (CIMIT) SPECIAL CONFERENCE + EXPO EVENTS! http://www.bioitworldexpo.com/boston03/V40/index.cvn?id=10182&p_navID=107 ============================================================== * Ernst & Young Venture Summit sponsored by IDG Ventures * Opening Night Networking Reception * Benjamin Franklin Award sponsored by Bionformatics.Org * Bio-IT World Best of Show Award * Over 90 companies showcasing the best solutions * Technology Showcase Presentations * Birds-of-a-Feather Meetings * BiotechTuesday Networking Event * Featured Track Speakers and Internationally Recognized Faculty DOWNLOAD THE CONFERENCE BROCHURE FOR FULL EVENT DETAILS ============================================================== http://www.bioitworldexpo.com/convdata/boston03/brochures/Bio-IT%20World%20Conference%20+%20Expo%20FINAL%20Brochure.pdf We look forward to seeing you in March! (All registration fees are non-refundable, including all cancellations, and credentials are transferable. This offer/discount is valid for one new registration only and must be redeemed/noted at time of initial registration. No refunds or credits will be issued for a discount after the initial registration. This offer cannot be duplicated, redeemed for cash, or used in conjunction with any other offer.) Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org President, Bioinformatics.Org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From j.g.rowland at imperial.ac.uk Sat Feb 21 12:28:02 2004 From: j.g.rowland at imperial.ac.uk (Rowland, John G A) Date: Sat, 21 Feb 2004 17:28:02 -0000 Subject: [BiO BB] database design question Message-ID: <10940CF26FF8064AA79668E9E94303B805EA7F@icex32.ic.ac.uk> I am currently in the process of building a small database in MS Access for the purposes of storing (in a computationally searchable format) protocol and results data from published and unpublished material. I would like to be able to search this database for a particular gene/protein and see all instances of its occurrence, regardless of the use of synonyms and not restrictiong it to only pulling out a specific Accession number. Unfortunately I am unsure of the best table/relationship setup to acheive this! Can anyone offer any insight into this problem? (I have googled and googled for about 6 months...) Regards, John -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 2613 bytes Desc: not available URL: From dmb at mrc-dunn.cam.ac.uk Thu Feb 26 18:11:07 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 26 Feb 2004 23:11:07 +0000 (GMT) Subject: [BiO BB] database design question In-Reply-To: <10940CF26FF8064AA79668E9E94303B805EA7F@icex32.ic.ac.uk> Message-ID: Database design is a big field! It is unlikely that you can find an 'out of the box' solution for what you want, but it is a good idea to search. Many books on data modeling (a way of fitting data to a particular design concept) exist, but many are based on principals of good design strategy rather than a particular design formula. I don't advise reading more than a few articles on database design (biological database design if you can find them). The best way I know is make one table for each concept in your data, so you have genes, give them a table - you mention synonyms, so make a synonym table, protocols = protocols table, results = results table. If each protocol has a special results set, then create a separate table for the results of each protocol. An implicit concept is that of an experiment which links a gene to a protocol and a set of results. as you develope the datbase I advise you constantly try to use it, and through an itterative process of design and use you converge on an optimal solution for your requirements. This is just my way of working, people will always argue different ways which suit them (or their aims) better. Cheers, Dan. On Sat, 21 Feb 2004, Rowland, John G A wrote: > I am currently in the process of building a small database in MS > Access for the purposes of storing (in a computationally searchable > format) protocol and results data from published and unpublished > material. > > I would like to be able to search this database for a particular > gene/protein and see all instances of its occurrence, regardless of > the use of synonyms and not restrictiong it to only pulling out a > specific Accession number. > > Unfortunately I am unsure of the best table/relationship setup to > acheive this! > > Can anyone offer any insight into this problem? (I have googled and > googled for about 6 months...) > > Regards, > > John > From aditi_ks at hotmail.com Thu Feb 26 19:39:21 2004 From: aditi_ks at hotmail.com (Aditi Kolachala) Date: Thu, 26 Feb 2004 16:39:21 -0800 Subject: [BiO BB] database design question Message-ID: I have used MS Access in the past and the software can really get to you, if you don't have a grasp of the heirarchial and structural relationship between different entities. The Conolly book on Database design and entity relationship might help elicit several details on such relationships. AK > >Database design is a big field! > >It is unlikely that you can find an 'out of the box' solution for what you >want, but it is a good idea to search. Many books on data modeling (a way >of fitting data to a particular design concept) exist, but many are based >on principals of good design strategy rather than a particular design >formula. I don't advise reading more than a few articles on database >design (biological database design if you can find them). > >The best way I know is make one table for each concept in your data, so >you have genes, give them a table - you mention synonyms, so make a >synonym table, protocols = protocols table, results = results table. If >each protocol has a special results set, then create a separate table for >the results of each protocol. An implicit concept is that of an experiment >which links a gene to a protocol and a set of results. > >as you develope the datbase I advise you constantly try to use it, and >through an itterative process of design and use you converge on an optimal >solution for your requirements. > >This is just my way of working, people will always argue different ways >which suit them (or their aims) better. > >Cheers, >Dan. > >On Sat, 21 Feb 2004, Rowland, John G A wrote: > > > I am currently in the process of building a small database in MS > > Access for the purposes of storing (in a computationally searchable > > format) protocol and results data from published and unpublished > > material. > > > > I would like to be able to search this database for a particular > > gene/protein and see all instances of its occurrence, regardless of > > the use of synonyms and not restrictiong it to only pulling out a > > specific Accession number. > > > > Unfortunately I am unsure of the best table/relationship setup to > > acheive this! > > > > Can anyone offer any insight into this problem? (I have googled and > > googled for about 6 months...) > > > > Regards, > > > > John > > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Protect your PC - get McAfee.com VirusScan Online http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 From mgruenb at gmx.net Fri Feb 27 04:17:38 2004 From: mgruenb at gmx.net (Michael Gruenberger) Date: Fri, 27 Feb 2004 09:17:38 +0000 Subject: [BiO BB] database design question In-Reply-To: <10940CF26FF8064AA79668E9E94303B805EA7F@icex32.ic.ac.uk> References: <10940CF26FF8064AA79668E9E94303B805EA7F@icex32.ic.ac.uk> Message-ID: <1077873458.3111.18.camel@vogel> Hi John, try searching for 'normalization'. Normalization is the process of designing a good data model. It's quite confusing the first few times you read through it, but after you've seen a few examples you should be able to create reasonably well designed databases. Once you've read a few tutorials, it might be a good idea to have a look at the example databases that come with Access to see how to create queries and reports that can handle more complicated data structures. However, from my experience (I teach Access for beginners) it's quite difficult to use Access once you have more than 3-4 related tables and you might have to use a different database system in the end. I guess once you have designed a good data model, post it to the list and I'm sure there are many people here who can help you fine tune it. Hope this helps! Cheers, Michael. On Sat, 2004-02-21 at 17:28, Rowland, John G A wrote: > I am currently in the process of building a small database in MS Access for the purposes of storing (in a computationally searchable format) protocol and results data from published and unpublished material. > > I would like to be able to search this database for a particular gene/protein and see all instances of its occurrence, regardless of the use of synonyms and not restrictiong it to only pulling out a specific Accession number. > > Unfortunately I am unsure of the best table/relationship setup to acheive this! > > Can anyone offer any insight into this problem? (I have googled and googled for about 6 months...) > > Regards, > > John -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From dmb at mrc-dunn.cam.ac.uk Fri Feb 27 05:24:07 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 27 Feb 2004 10:24:07 +0000 (GMT) Subject: [BiO BB] database design question In-Reply-To: <1077873458.3111.18.camel@vogel> Message-ID: On Fri, 27 Feb 2004, Michael Gruenberger wrote: > Hi John, > > However, from my experience (I teach Access for beginners) it's quite > difficult to use Access once you have more than 3-4 related tables and > you might have to use a different database system in the end. I have found ODBC between mysql and access is really good, allowing easy interchange between the two systems. From prathibha_562 at yahoo.co.in Fri Feb 27 06:51:05 2004 From: prathibha_562 at yahoo.co.in (=?iso-8859-1?q?prathibha=20bharathi?=) Date: Fri, 27 Feb 2004 11:51:05 +0000 (GMT) Subject: [BiO BB] database design question In-Reply-To: Message-ID: <20040227115105.29383.qmail@web8203.mail.in.yahoo.com> Mr John: Just go to PIR website(Don't know URL,u can reach there through GOOgle).There You can find their schema for their relation Database for MySQL.You can get some idea on seeing this schema for your database.If ur main aim is Database search, u can use thier Database itself. Hope this may help you Prathibha. _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more. -------------- next part -------------- An HTML attachment was scrubbed... URL: From pooja at igc.gulbenkian.pt Fri Feb 27 09:41:09 2004 From: pooja at igc.gulbenkian.pt (Pooja Jain) Date: Fri, 27 Feb 2004 14:41:09 -0000 (WET) Subject: [BiO BB] database design question In-Reply-To: <35083.194.117.22.137.1077888471.squirrel@webmail.igc.gulbenkian.pt> References: <10940CF26FF8064AA79668E9E94303B805EA7F@icex32.ic.ac.uk> <1077873458.3111.18.camel@vogel> <35083.194.117.22.137.1077888471.squirrel@webmail.igc.gulbenkian.pt> Message-ID: <38776.194.117.22.137.1077892869.squirrel@webmail.igc.gulbenkian.pt> Hi John, About four months back I was in the same state as you are. Then I decided to use MySQL and it went fine with me. Its very easy, even for novice and you will get very good manuals/Tutorials (online and books) to learn it. You can use Google to find the one that suites you. Though, you can start from www.mysql.com. Although I never used MS Access, but I can assure you using MySQL will not be difficult. Once you have done with the conceptual model (class or entity diagram) as other list members have also suggested, you can easily convert it to a relational model using MySQL data model. MySQL is providing new feature with its every new release where various integrity constraints are being solved gradually. Also handling more tables is not a problem with it. Making Queries across multiple table and collecting fields for different tables in a single result set is quite easy. I am not an advanced user of MySQL but certainly it has some exceptional features (that I am in process of learning !) that has made it so popular. Moreover, with the growth of java and the rise of database-powred web applications, in future you may need to use java as well as may want to write small PHP scripts. These two technologies goes well with MySQL. Following book will be a great help for you to start: "Understanding SQL and Java Together - A Guide to SQLJ, JDBC, and Related Technologies" Authors : Jim Melton and Andrew Eisenberg Morgan Kaufmann Publishers. Good Luck. -Pooja > > > On Sat, 2004-02-21 at 17:28, Rowland, John G A wrote: >> I am currently in the process of building a small database in MS Access >> for the > purposes of storing (in a computationally searchable format) protocol and > results > data from published and unpublished material. >> >> I would like to be able to search this database for a particular >> gene/protein and > see all instances of its occurrence, regardless of the use of synonyms and > not > restrictiong it to only pulling out a specific Accession number. >> >> Unfortunately I am unsure of the best table/relationship setup to >> acheive this! >> >> Can anyone offer any insight into this problem? (I have googled and >> googled for > about 6 months...) >> >> Regards, >> >> John > From golharam at umdnj.edu Thu Feb 26 18:23:20 2004 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 26 Feb 2004 18:23:20 -0500 Subject: [BiO BB] RE: database design question In-Reply-To: <10940CF26FF8064AA79668E9E94303B805EA7F@icex32.ic.ac.uk> Message-ID: <004b01c3fcbf$86299110$6d00a8c0@GOLHARMOBILE1> Unfortunately its not that easy. Will all the synonyms of the gene/protein exist in the database? What is a computationally searchable format? What are you going to be searching on/for in particular? ----- Ryan Golhar Analyst II The Informatics Institute at The University of Medicine & Dentistry of NJ Phone: 973-972-5034 Fax: 973-972-7412 Email: golharam at umdnj.edu -----Original Message----- From: Rowland, John G A [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Rowland, John G A Sent: Saturday, February 21, 2004 12:28 PM To: bio_bulletin_board at bioinformatics.org Subject: database design question I am currently in the process of building a small database in MS Access for the purposes of storing (in a computationally searchable format) protocol and results data from published and unpublished material. I would like to be able to search this database for a particular gene/protein and see all instances of its occurrence, regardless of the use of synonyms and not restrictiong it to only pulling out a specific Accession number. Unfortunately I am unsure of the best table/relationship setup to acheive this! Can anyone offer any insight into this problem? (I have googled and googled for about 6 months...) Regards, John From uthrar at psu.edu Thu Feb 26 18:52:59 2004 From: uthrar at psu.edu (Uthra Ramaswamy) Date: Thu, 26 Feb 2004 18:52:59 -0500 (EST) Subject: [BiO BB] clustalw Message-ID: <200402262352.SAA03022@webmail9.cac.psu.edu> Hi Has anyone used Clustalw in the profile alignment mode? I tried to and found that none of the menu items except the first one work. I downloaded the latest version (1.83 for DOS) but it seems to have the same problem. If anyone has successfully used Clustalw in the profile alignment mode could you please let me know how you went about it? Thanks! Uthra Ramaswamy From mourad12345678 at yahoo.com Sat Feb 28 01:22:52 2004 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Fri, 27 Feb 2004 22:22:52 -0800 (PST) Subject: [BiO BB] CfP : Algorithms in Molecular Biology (ALBIO'04) Message-ID: <20040228062252.91233.qmail@web12303.mail.yahoo.com> CALL FOR PAPERS Algorithms in Molecular Biology (ALBIO'04) Session of 6th Int.Conf. on Algorithms, Scientific Computing, Modelling and Simulation (ASCOMS'04) Cancun, Mexico, May 12-15, 2004 http://www.worldses.org/conferences/2004/mexico/ascoms/index.html Computational Molecular Biology, has emerged from the Human Genome Project as an important discipline for academic research and industrial application. The growing size of biological databases, the complexity of biological problems and the necessity to deal with errors in biological sequences all result in large run time and memory requirements. Biological sequence databases are growing at an exponential rate. All of these factors will make the development of fast, low memory requirements and high-performances algorithms increasingly important in Computational Molecular Biology. In our session, we are interested in papers that deal with all aspects of algorithms in Molecular Biology. We are, particularly, interested in algorithms that address fundamental and/or applied problems in Molecular Biology, that are computationally efficient, that have been implemented and experimented on simulated and/or on real biological sequences and that provide interesting new results. The submitted papers should present recent research results and identify and explore directions for future research. Topics include, but not limited to: (i) strings processing, (ii) biological sequences comparison, (iii) structures prediction, (iv) phylogeny reconstruction, (v) DNA sequences assembly, clustering, and mapping, (vi) molecular evolution, (vii) genes prediction/recognition, (viii) genes expression INSTRUCTIONS TO AUTHORS You are invited to submit a hardcopy or a pdf version of a draft paper, about 4 to 5 pages including figures and references, before April 2, 2004 to the Session Chair : Dr. Mourad Elloumi : Mailing Address : Cit? Intilak bloc 6, app. 7, El Menzah 6, 2091 Tunis, Tunisia. Mobile: +216 98 468 859 Phone : +216 71 233 253 E.Mail: Mourad.Elloumi at fsegt.rnu.tn how to send your paper? please, fill in the form http://www.worldses.org/conferences/2004/mexico/internet.htm and declare that your paper belong to this session __________________________________ Do you Yahoo!? Get better spam protection with Yahoo! Mail. http://antispam.yahoo.com/tools