From kanzure at gmail.com Sat Mar 1 07:00:28 2008 From: kanzure at gmail.com (Bryan Bishop) Date: Sat, 1 Mar 2008 06:00:28 -0600 Subject: [BiO BB] MyJournals.org In-Reply-To: <007f01c87b00$2f3380a0$6bfdfea9@Tim> References: <007f01c87b00$2f3380a0$6bfdfea9@Tim> Message-ID: <200803010600.29388.kanzure@gmail.com> On Friday 29 February 2008, Tim Hulsen wrote: > Do you want to have easy access to the latest issues of your > favourite journals, from all over the world, just through your web > browser? > > Please visit http://www.myjournals.org , create a login and make your > pick from the 422 journals currently available. This isn't easy. It still costs. Rather discriminatory, eh? - Bryan ________________________________________ Bryan Bishop http://heybryan.org/ From bsmagic at gmail.com Mon Mar 3 01:28:10 2008 From: bsmagic at gmail.com (Sheng Wang) Date: Mon, 3 Mar 2008 14:28:10 +0800 Subject: [BiO BB] MyJournals.org In-Reply-To: <200803010600.29388.kanzure@gmail.com> References: <007f01c87b00$2f3380a0$6bfdfea9@Tim> <200803010600.29388.kanzure@gmail.com> Message-ID: <793f8aed0803022228t4989d666o4b7d928f596a6dc3@mail.gmail.com> Great? On 3/1/08, Bryan Bishop wrote: > > On Friday 29 February 2008, Tim Hulsen wrote: > > Do you want to have easy access to the latest issues of your > > favourite journals, from all over the world, just through your web > > browser? > > > > Please visit http://www.myjournals.org , create a login and make your > > pick from the 422 journals currently available. > > This isn't easy. It still costs. Rather discriminatory, eh? > > - Bryan > ________________________________________ > Bryan Bishop > http://heybryan.org/ > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Best Regards Sheng Wang From avinash at lanl.gov Wed Mar 5 14:07:09 2008 From: avinash at lanl.gov (Avinash Kewalramani) Date: Wed, 05 Mar 2008 12:07:09 -0700 Subject: [BiO BB] Request/Call for papers at BIOCOMP (WORLDCOMP) Message-ID: <47CEEF5D.5070309@lanl.gov> Respected Ladies and Gentlemen, First an introduction of myself. I am a Technical Staff Member at Los Alamos National Laboratory working on distributed computing infrastructures for BioInformtics applications. We are organizing a session in a well known conference named BIOCOMP part of WORLDCOMP http://www.world-academy-of-science.org/worldcomp08/ws/conferences/biocomp08 and the session information is below. We would like to invite you to participate in this session by submitting research papers, report, talks or poster presentations. Also if you know of any students or colleagues who would be interested please feel free to forward it to them too. Your support for this will be highly appreciated. The rough drafts of the papers are due by March 15th. Please do get in touch with me if you have any questions. Thanks and Regards Avinash /*Title of Approved Session: * High Performance Computing Architectures for Bioinformatics Applications * Chair of Session: * Avinash Kewalramani Los Alamos National Laboratory, USA //avinash at lanl.gov/ / * Conference: * The 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08: July 14-17, 2008, Monte Carlo Resort, Las Vegas, USA) / /*Topic for the conference*/ /Bionformatics applications possess characteristics such as being resource intensive and proprietary in nature. Resource intensiveness needs to be handled by making the applications distributed. Proprietary and legacy systems need to be integrated across organizational ownership boundaries. The future of bioinformatics will benefit from an "on demand" high performance computing infrastructure that appears seamless to the sophisticated bioinformatics user. / Topics of interest which would help in achieving the above goal include but are not limited to: * Parallel algorithms/databases and their applications to biological systems. * Distributed bioinformatics systems using cluster computing and/or supercomputers. * Distributed architectures for biological applications * Grid computing architectures for biological applications. * Service oriented architectures for integrating legacy biological applications * Providing Bioinformatics services using Java Web services. * Providing Bioinformatics web services using Windows Communication Foundation * /Providing Bioinformatics web services using service based technologies like XML-RPC,DCOM,CORBA etc./ From ulimard at yahoo.com.br Wed Mar 5 14:09:03 2008 From: ulimard at yahoo.com.br (Ulisses Dias) Date: Wed, 5 Mar 2008 16:09:03 -0300 (ART) Subject: [BiO BB] Clustal Gap Penalties Message-ID: <392994.74647.qm@web56615.mail.re3.yahoo.com> Hi all, I'm trying to understand the clustal gap penalties that is in Thompson, 94, but It's very hard to do so without examples and so on. Anyone knows where I can find a detailed explanation about it? Best regards --------------------------------- Abra sua conta no Yahoo! Mail, o ?nico sem limite de espa?o para armazenamento! From iain.m.wallace at gmail.com Thu Mar 6 00:17:18 2008 From: iain.m.wallace at gmail.com (Iain Wallace) Date: Thu, 6 Mar 2008 00:17:18 -0500 Subject: [BiO BB] Clustal Gap Penalties In-Reply-To: <392994.74647.qm@web56615.mail.re3.yahoo.com> References: <392994.74647.qm@web56615.mail.re3.yahoo.com> Message-ID: <8cff3eb80803052117u68e2bf57t770512fc68b63666@mail.gmail.com> Hi, ClustalW uses an affine gap penalty which means that it is harder to open a gap than extending a gap. There are two parameters a gap opening penalty and a gap extension penalty. This is discussed in more detail here http://homepage.usask.ca/~ctl271/857/affine_gap_penalties.shtml. I think the actual algortihm implementation is described by Gotoh (1990 PMID:2165832) and the group to group alignment stage (moving from pairwise alignment to groups of sequence alignment) is described by Gotoh (1994, PMID: 7804871) It also scales these two parameters based on the substitution matrix that is used for the alignment. There are also a couple of methods for increasing/decreasing these scores depending on the context of the sequence such as secondary structure or terminal gaps, which are discussed in the help manual, http://align.genome.jp/clustalw/clustalw_help.html Hope this helps Iain On Wed, Mar 5, 2008 at 2:09 PM, Ulisses Dias wrote: > Hi all, > > I'm trying to understand the clustal gap penalties that is in Thompson, > 94, but It's very hard to do so without examples and so on. Anyone knows > where I can find a detailed explanation about it? > > Best regards > > > --------------------------------- > Abra sua conta no Yahoo! Mail, o ?nico sem limite de espa?o para > armazenamento! > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From harry.mangalam at uci.edu Thu Mar 6 15:39:25 2008 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Thu, 6 Mar 2008 12:39:25 -0800 Subject: [BiO BB] expression level by EST by family Message-ID: <200803061239.25142.harry.mangalam@uci.edu> Posting for a colleague: I'm looking for tools to do a little data mining in the NCBI data base. Specifically what I'm interested in is obtaining the EST frequency as a measure of the expression levels of members of a particular gene family (Na/K ATPases) by organism (mouse) and tissue type (heart). I've browsed the EST database and it looks like the data is in there but what I need is a tool that can search all records in each relevant data base. Any ideas or pointers in the right direction? It sounds like what he needs is an SQL-like interface to dbEST; is there such a thing extant or is this something that will have to be writ using a bio* toolkit to NCBI's or other API? It does look like Ensembl's Biomart could answer questions like this tho - can anyone confirm? -- Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824 0084(o), 949 285 4487(c) -- [A Nation of Sheep breeds a Government of Wolves. Edward R. Murrow] From harry.mangalam at uci.edu Fri Mar 7 14:07:32 2008 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Fri, 7 Mar 2008 11:07:32 -0800 Subject: [BiO BB] expression level by EST by family Message-ID: <200803071107.32140.harry.mangalam@uci.edu> (apologies if this posted 2x - possible mail burp) Posting for a colleague: I'm looking for tools to do a little data mining in the NCBI data base. Specifically what I'm interested in is obtaining the EST frequency as a measure of the expression levels of members of a particular gene family (Na/K ATPases) by organism (mouse) and tissue type (heart). I've browsed the EST database and it looks like the data is in there but what I need is a tool that can search all records in each relevant data base. Any ideas or pointers in the right direction? It sounds like what he needs is an SQL-like interface to dbEST; is there such a thing extant or is this something that will have to be writ using a bio* toolkit to NCBI's or other API? It does look like Ensembl's Biomart could answer questions like this tho - can anyone confirm? -- Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824 0084(o), 949 285 4487(c) -- [A Nation of Sheep breeds a Government of Wolves. Edward R. Murrow] From marchywka at hotmail.com Sun Mar 9 19:16:32 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Sun, 9 Mar 2008 19:16:32 -0400 Subject: [BiO BB] sample code available for download Message-ID: Hi, I had gotten some interest in the code that I mentioned in prior posts. I was working on a website-related project so I thought I would go ahead and make sample code available. If you go to this link, http://www.spottext.com/marchywka/distroform.cfm you will get a very short set of examples followed by a rather non-professional-by-design disclaimer and then a form. The form requests an e-mail address to which zip files can be downloaded. All of this stuff is very much "in-progress" and certainly NOT documented to any great extent ( there were a couple pieces of code I needed to fix/comment out to get "make all" to complete cleanly but everything finally did seem to build. I am aware, however, of at least one hard coded path and there are probably a bunch of little things that would need to be adapted. The scripts may not all function as I excluded many special purpose support scripts for idiosyncratic features. There are some easily identifiable paths that you would have to change too ). There may also be a variety of "dead-end" code pieces that I may have left in even though they are no longer useful for anything. Personally, I think some of the string processing stuff is interesting but otherwise not too sure. The makefiles pretty much document what is available and the scripts download contains some ",doc" files that may be of assistance. I am currently blocking gmail,hotmail, and yahoo to test some db features but I'm not sure when to open these up- if you have an ISP or institutional address that would help. I hope to record the mail addresses and related request info just for reference and testing. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on marchywka at yahoo.com if no reply here. Thanks. _________________________________________________________________ Climb to the top of the charts!?Play the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_jan From kechatt at gmail.com Sun Mar 9 00:42:19 2008 From: kechatt at gmail.com (ke chatterjee) Date: Sat, 8 Mar 2008 21:42:19 -0800 Subject: [BiO BB] multiple sequence analysis through ClustalW Message-ID: <447c66730803082142y2b90ef79k72140cc67c4a35cd@mail.gmail.com> why the all 'A' are in red color and other 'C, T, G' are in green color in the result of multiple sequence analysis using ClustalW? Please send reply to bony_chatt at yahoo.com From dan.bolser at gmail.com Wed Mar 12 07:22:16 2008 From: dan.bolser at gmail.com (dan.bolser at gmail.com) Date: Wed, 12 Mar 2008 11:22:16 +0000 Subject: [BiO BB] dan.bolser has invited you to Spokeo Message-ID: <47d7bce84a3ee_47881c1766dabf085395d@mongrel2.tmail> Hi General,

dan.bolser at gmail.com has invited you to Spokeo, which finds your friends' updates across the Web. On average, Spokeo finds 87 friends across 30 different social networks. See what Spokeo can find for you now! Click http://www.spokeo.com/public/join?c=d01cd4ad2c06a0074f2f8cfd01cbf8b081e75d53 to accept your invitation. ----- This invitation was sent with dan.bolser's approval. If you wish to opt out of all future emails, go to http://www.spokeo.com/optout?c=b495256575751575349 Copyright (c) 2008 Spokeo, Inc. All rights reserved. 1685 Plymouth Street #200, Mountain View, CA 94043 From barry.hardy at vtxmail.ch Thu Mar 13 01:35:41 2008 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Thu, 13 Mar 2008 06:35:41 +0100 Subject: [BiO BB] eCheminfo Hands-on Drug Discovery Workshop in Oxford Message-ID: <47D8BD2D.8040508@vtxmail.ch> The 5 Day eCheminfo Hands-on Drug Discovery Workshop Week will take place this year 21-25 July 2008 at the Medical Sciences Teaching Center, Oxford University, Oxford, UK. Topics to be covered include Virtual Screening & Docking; Structure-based Drug Design; Ligand Optimisation & Library Design; Structure Search, Similarity and Property Estimation; Data Mining, Analysis & Visualisation; Pharmacophore Modelling for Lead Identification; Fragment-based Drug Design; QSAR-based Predictive Toxicology; and Quantitative Spectrometric Data-Activity Relationship Modelling. These workshops are aimed to provide a set of stimulating workshops using latest advanced modelling techniques of relevance to chemists, life scientists and modellers working in drug discovery. The workshop group studies problems with hands-on examples using leading-edge software and discusses complex issues highlighted by examples and case studies presented by instructors. A variety of leading drug discovery software packages and an IT classroom are used by instructors and participants to work through problems. Bursary: A Bursary Award sponsored by Tripos will be used to support the attendance of one academic participant, who may be working in any area of research related to drug discovery. To apply for the bursary please send an email with a) description of your research (ca. 500 words); b) your training needs (ca. 500 words), c) your CV to echeminfo -[at]- douglasconnect.com by 15 April 2008. The recipient of the award will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of the training on their research progress and will be notified by 30 April. We gratefully acknowledge the sponsorship support of Tripos. More Information: Web: http://echeminfo.colayer.net/COMTY_training Blog: http://barryhardy.blogs.com/cheminfostream best regards Barry Hardy eCheminfo Community of Practice Douglas Connect Switzerland Tel: +41 61 851 0170 From mmiller at mail.usp.edu Sat Mar 15 13:30:36 2008 From: mmiller at mail.usp.edu (mmiller at mail.usp.edu) Date: Sat, 15 Mar 2008 17:30:36 +0000 Subject: [BiO BB] Fungal genefinding hints needed Message-ID: Hello, BBB. A am trying to annotate a recently completed fungal genome. I have been able to train GLimmerHMM against Aspergillus, scan my genome and generate a list of exons. But that's the extent of my experience so far. ? Are the other genefinders I should be trying? I had trouble compiling GeneZilla. ? Are there existing programs that can use a genomic FASTA file and Glimmer coordinates to write out protein sequences in FASTA format? Or do people in my position usually write their own script? ? Are there good on-line discussion groups for this sort of topic? Thanks, Mark From mmuratet at hudsonalpha.org Mon Mar 17 16:48:00 2008 From: mmuratet at hudsonalpha.org (Michael Muratet) Date: Mon, 17 Mar 2008 15:48:00 -0500 Subject: [BiO BB] Fungal genefinding hints needed In-Reply-To: References: Message-ID: Mark How about TwinScan? It employs the concept of an 'informant' database which in this case would be C. neoformans (as I recall). Good luck Mike On Mar 15, 2008, at 12:30 PM, wrote: > > Hello, BBB. > > A am trying to annotate a recently completed fungal genome. I have > been able to train GLimmerHMM against Aspergillus, scan my genome > and generate a list of exons. But that's the extent of my > experience so far. > > ? Are the other genefinders I should be trying? I had trouble > compiling GeneZilla. > ? Are there existing programs that can use a genomic FASTA file and > Glimmer coordinates to write out protein sequences in FASTA format? > Or do people in my position usually write their own script? > ? Are there good on-line discussion groups for this sort of topic? > > Thanks, > Mark > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From marty.gollery at gmail.com Mon Mar 17 17:06:10 2008 From: marty.gollery at gmail.com (Martin Gollery) Date: Mon, 17 Mar 2008 14:06:10 -0700 Subject: [BiO BB] Fungal genefinding hints needed In-Reply-To: References: Message-ID: Hi Mark, Take a look at the Fungal HMM database (FPfam) which was written up last year in BMC genomics. Cheers, Marty A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. Alam I, Hubbard SJ, Oliver SG, Rattray M. School of Computer Science, University of Manchester, Kilburn Building, Manchester, UK. intikhab.alam at manchester.ac.uk On Sat, Mar 15, 2008 at 10:30 AM, wrote: > > Hello, BBB. > > A am trying to annotate a recently completed fungal genome. I have been able to train GLimmerHMM against Aspergillus, scan my genome and generate a list of exons. But that's the extent of my experience so far. > > ? Are the other genefinders I should be trying? I had trouble compiling GeneZilla. > ? Are there existing programs that can use a genomic FASTA file and Glimmer coordinates to write out protein sequences in FASTA format? Or do people in my position usually write their own script? > ? Are there good on-line discussion groups for this sort of topic? > > Thanks, > Mark > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist TimeLogic- a Division of Active Motif 775-833-9113 880 Northwood Blvd. Suite 7 Incline Village, NV 89451 From sariego9 at yahoo.com Mon Mar 17 17:59:55 2008 From: sariego9 at yahoo.com (Diego Martinez) Date: Mon, 17 Mar 2008 14:59:55 -0700 (PDT) Subject: [BiO BB] Fungal genefinding hints needed Message-ID: <169256.85231.qm@web32506.mail.mud.yahoo.com> Hello Mark, you might also try softberry.com, they make the popular fgenes and fgenesh programs, and I believe they have a web interface. also, genewise in the wise2 package might be helpful, you can get to that (and download) at ebi. also, augustus http://augustus.gobics.de/ has been popular lately, but I have not tried it personally. I think in EMBOSS there is a dna - protein translator, you can use that. I can go on about the genefinders if needed. we used to use many different ones, and then choose the best for each locus using a filtering scheme. Diego ----- Original Message ---- From: "mmiller at mail.usp.edu" To: bbb at bioinformatics.org Sent: Saturday, March 15, 2008 11:30:36 AM Subject: [BiO BB] Fungal genefinding hints needed Hello, BBB. A am trying to annotate a recently completed fungal genome. I have been able to train GLimmerHMM against Aspergillus, scan my genome and generate a list of exons. But that's the extent of my experience so far. ? Are the other genefinders I should be trying? I had trouble compiling GeneZilla. ? Are there existing programs that can use a genomic FASTA file and Glimmer coordinates to write out protein sequences in FASTA format? Or do people in my position usually write their own script? ? Are there good on-line discussion groups for this sort of topic? Thanks, Mark _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From c.klaassen at cwz.nl Wed Mar 19 03:45:38 2008 From: c.klaassen at cwz.nl (=?windows-1252?Q?=22Corn=E9_H=2EW=2E_Klaassen=22?=) Date: Wed, 19 Mar 2008 08:45:38 +0100 Subject: [BiO BB] tree viewing software Message-ID: <47E0C4A2.3040808@cwz.nl> dear All, Recently I tried to use treeview to display an unrooted tree of some 2500 sequences and obtained a "Label hash table overflow" error message. I guess 2500 is just too many. Can anybody recommend other freeware that will be able to get the job done? Thanks for your reactions! Corn? -- dr. Corn? H.W. Klaassen ? Molecular Biologist Dept. Clinical Chemistry, C60 Dept. Medical Microbiology & Infectious Diseases, C70 Canisius Wilhelmina Hospital, Weg door Jonkerbos 100, 6532 SZ Nijmegen, The Netherlands T: 31(0)243657514 (office); T: 31(0)243658677 (direct) F: 31(0)243657516; E: c.klaassen at cwz.nl ========================================== Dit bericht is uitsluitend bestemd voor de geadresseerde. Het bericht kan vertrouwelijke informatie bevatten. Als u dit bericht per abuis hebt ontvangen, wordt u verzocht onmiddellijk de afzender te informeren. Ook verzoeken wij u het bericht te vernietigen en de inhoud niet onder derden te verspreiden of te gebruiken. This message is intended exclusively for the addressee. It may contain information that is confidential. If you are not the intended recipient, we request that you notify the sender immediately. In that case, we also request that you destroy the message and that you neither use the contents nor disclose them in any manner to third parties. ========================================== From marchywka at hotmail.com Thu Mar 20 17:00:28 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Thu, 20 Mar 2008 17:00:28 -0400 Subject: [BiO BB] Fungal genefinding hints needed In-Reply-To: <169256.85231.qm@web32506.mail.mud.yahoo.com> References: <169256.85231.qm@web32506.mail.mud.yahoo.com> Message-ID: Do you have a link to some training/testing sets? I think one was mentioned for the hmmer discussed by the original poster but wasn't sure what resources there are in this area. Are there examples of known cases that are particularly confusing? Thanks. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Mon, 17 Mar 2008 14:59:55 -0700 > From: sariego9 at yahoo.com > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] Fungal genefinding hints needed > > Hello Mark, > > you might also try softberry.com, they make the popular fgenes and fgenesh programs, and I believe they have a > web interface. also, genewise in the wise2 package might be helpful, you can get to that (and download) at ebi. > also, augustus http://augustus.gobics.de/ has been popular lately, but I have not tried it personally. I think in EMBOSS there is a dna - protein translator, > you can use that. > I can go on about the genefinders if needed. we used to use many different ones, and then choose the best for each locus using a filtering scheme. > > Diego > > > ----- Original Message ---- > From: "mmiller at mail.usp.edu" > To: bbb at bioinformatics.org > Sent: Saturday, March 15, 2008 11:30:36 AM > Subject: [BiO BB] Fungal genefinding hints needed > > > Hello, BBB. > > A am trying to annotate a recently completed fungal genome. I have been able to train GLimmerHMM against Aspergillus, scan my genome and generate a list of exons. But that's the extent of my experience so far. > > ? Are the other genefinders I should be trying? I had trouble compiling GeneZilla. > ? Are there existing programs that can use a genomic FASTA file and Glimmer coordinates to write out protein sequences in FASTA format? Or do people in my position usually write their own script? > ? Are there good on-line discussion groups for this sort of topic? > > Thanks, > Mark > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Windows Live Hotmail is giving away Zunes. http://www.windowslive-hotmail.com/ZuneADay/?locale=en-US&ocid=TXT_TAGLM_Mobile_Zune_V3 From nuin at genedrift.org Thu Mar 20 16:45:26 2008 From: nuin at genedrift.org (Paulo Nuin) Date: Thu, 20 Mar 2008 16:45:26 -0400 Subject: [BiO BB] tree viewing software In-Reply-To: <47E0C4A2.3040808@cwz.nl> References: <47E0C4A2.3040808@cwz.nl> Message-ID: <47E2CCE6.1010004@genedrift.org> Hi Corne Try Dendroscope. http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/welcome.html Cheers Paulo Corn? H.W. Klaassen wrote: > dear All, > > Recently I tried to use treeview to display an unrooted tree of some > 2500 sequences and obtained a "Label hash table overflow" error message. > I guess 2500 is just too many. Can anybody recommend other freeware that > will be able to get the job done? > > Thanks for your reactions! > > Corn? > > From hlapp at gmx.net Thu Mar 20 18:22:59 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 20 Mar 2008 18:22:59 -0400 Subject: [BiO BB] tree viewing software In-Reply-To: <47E0C4A2.3040808@cwz.nl> References: <47E0C4A2.3040808@cwz.nl> Message-ID: <704D3828-D5D7-416D-9050-5174F70912F3@gmx.net> Have you tried FigTree? http://tree.bio.ed.ac.uk/software/figtree/ On Mar 19, 2008, at 3:45 AM, Corn? H.W. Klaassen wrote: > dear All, > > Recently I tried to use treeview to display an unrooted tree of some > 2500 sequences and obtained a "Label hash table overflow" error > message. > I guess 2500 is just too many. Can anybody recommend other freeware > that > will be able to get the job done? > > Thanks for your reactions! > > Corn? > > -- > dr. Corn? H.W. Klaassen ? Molecular Biologist > Dept. Clinical Chemistry, C60 > Dept. Medical Microbiology & Infectious Diseases, C70 > Canisius Wilhelmina Hospital, Weg door Jonkerbos 100, > 6532 SZ Nijmegen, The Netherlands > T: 31(0)243657514 (office); T: 31(0)243658677 (direct) > F: 31(0)243657516; E: c.klaassen at cwz.nl > > > > ========================================== > > Dit bericht is uitsluitend bestemd voor de geadresseerde. > Het bericht kan vertrouwelijke informatie bevatten. > Als u dit bericht per abuis hebt ontvangen, wordt u > verzocht onmiddellijk de afzender te informeren. Ook > verzoeken wij u het bericht te vernietigen en de inhoud > niet onder derden te verspreiden of te gebruiken. > > This message is intended exclusively for the addressee. > It may contain information that is confidential. > If you are not the intended recipient, we request that > you notify the sender immediately. In that case, we > also request that you destroy the message and that > you neither use the contents nor disclose them in any > manner to third parties. > ========================================== > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Mar 20 18:50:52 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 20 Mar 2008 18:50:52 -0400 Subject: [BiO BB] tree viewing software In-Reply-To: <47E2CCE6.1010004@genedrift.org> References: <47E0C4A2.3040808@cwz.nl> <47E2CCE6.1010004@genedrift.org> Message-ID: Just FYI, Dendroscope is free as in beer for academics, but not free as in speech. -hilmar On Mar 20, 2008, at 4:45 PM, Paulo Nuin wrote: > Hi Corne > > Try Dendroscope. > > http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/ > welcome.html > > Cheers > > Paulo > > > > Corn? H.W. Klaassen wrote: >> dear All, >> >> Recently I tried to use treeview to display an unrooted tree of some >> 2500 sequences and obtained a "Label hash table overflow" error >> message. >> I guess 2500 is just too many. Can anybody recommend other >> freeware that >> will be able to get the job done? >> >> Thanks for your reactions! >> >> Corn? >> >> > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From nuin at terra.com.br Fri Mar 21 11:43:04 2008 From: nuin at terra.com.br (Paulo Nuin) Date: Fri, 21 Mar 2008 11:43:04 -0400 Subject: [BiO BB] tree viewing software In-Reply-To: References: <47E0C4A2.3040808@cwz.nl> <47E2CCE6.1010004@genedrift.org> Message-ID: <47E3D788.5030407@terra.com.br> Hi Didn't know about that. If you can point the source of that I'd appreciate, because I searched everywhere and couldn't find any mention of Dendroscope not being free for non-academics. Thanks a lot. Paulo Hilmar Lapp wrote: > Just FYI, Dendroscope is free as in beer for academics, but not free > as in speech. > > -hilmar > > On Mar 20, 2008, at 4:45 PM, Paulo Nuin wrote: > >> Hi Corne >> >> Try Dendroscope. >> >> http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/ >> welcome.html >> >> Cheers >> >> Paulo >> >> >> >> Corn? H.W. Klaassen wrote: >> >>> dear All, >>> >>> Recently I tried to use treeview to display an unrooted tree of some >>> 2500 sequences and obtained a "Label hash table overflow" error >>> message. >>> I guess 2500 is just too many. Can anybody recommend other >>> freeware that >>> will be able to get the job done? >>> >>> Thanks for your reactions! >>> >>> Corn? >>> >>> >>> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > From hlapp at gmx.net Sat Mar 22 13:21:23 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 22 Mar 2008 13:21:23 -0400 Subject: [BiO BB] tree viewing software In-Reply-To: <47E3D788.5030407@terra.com.br> References: <47E0C4A2.3040808@cwz.nl> <47E2CCE6.1010004@genedrift.org> <47E3D788.5030407@terra.com.br> Message-ID: <383661DD-94A9-47D6-A203-FAB3AF2E7964@gmx.net> On Mar 21, 2008, at 11:43 AM, Paulo Nuin wrote: > Hi > > Didn't know about that. If you can point the source of that I'd > appreciate, because I searched everywhere and couldn't find any > mention > of Dendroscope not being free for non-academics. Actually you are correct, there is indeed no stated distinction that I can find. Sorry if this caused any confusion. I probably read too many license and use statements :) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From sanchez at cis.jhu.edu Mon Mar 24 23:17:15 2008 From: sanchez at cis.jhu.edu (Francisco Sanchez) Date: Mon, 24 Mar 2008 23:17:15 -0400 (EDT) Subject: [BiO BB] inbred strains of model organisms Message-ID: <50353.71.248.89.11.1206415035.squirrel@webmail.cis.jhu.edu> Hello everybody, We are trying to assemble high-dimensional datasets to be used in modeling how SNPs, gene expression and copy number variation interact to produce a phenotype. We would like to collect such data for a large number of inbred strains of a model organism, such as mouse, rat or yeast. Does anyone know of good sources for such data? Any help will be greatly appreciated! Francisco Sanchez PhD student Johns Hopkins University From hlapp at gmx.net Fri Mar 28 00:47:19 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 28 Mar 2008 00:47:19 -0400 Subject: [BiO BB] NESCent Computational Phyloinformatics Course July 24 - Aug 4 Message-ID: <3153D1D9-09AB-4E95-9B1E-B2FC68085968@gmx.net> Computational Phyloinformatics: A Course at NESCent. 24 July - 4 August 2008 http://www.nescent.org/courses/2008/comphy/ Course Director: William Piel (piel at treebase.org) Course Administrator: Jory Weintraub (jory at nescent.org) Organizing Committee: Hilmar Lapp, William Piel, Todd Vision, Jory Weintraub Computational Phyloinformatics is a 10-day summer course sponsored by and held at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina (USA) that aims to give students practical knowledge and hands-on skills in phyloinformatics. SYNOPSIS Biologists are faced with ever-larger datasets, more complex evolutionary models, and more elaborate analytical methods. Seldom is it sufficient to run a dataset through an off-the-shelf program on a desktop PC; increasingly, biologists need to write scripts to interface with internet services and databases, build analytical pipelines, customize analyses, and distribute computation over multiple processors. This course is designed for graduate students, postdocs, and researchers in phylogenetics interested in receiving practical, hands-on training in the use of Perl, Java, or R for phyloinformatics applications. The course is divided into three parts: - Part I: A tutorial review of either Perl, Java, or R (while optional, this part is strongly recommended). - Part II: Students have the choice of pursuing (1) a Perl track, with focus on BioPerl and Bio::Phylo; (2) a Java track, with focus on how to write a Mesquite module and program workflows that utilize Mesquite modules; or (3) an R track, with a focus on comparative phylogenetic analysis using the libraries Ape, Ouch, and Phylobase. - Part III: Students choose between (1) a database track (with focus on SQL, BioSQL and database queries of phylogenetic trees); (2) a HyPhy track (with focus on scripting molecular evolution hypothesis tests in a phylogenetic framework); or (3) an advanced R track (with focus on automating analyses using vectorized calculations, advanced plotting and animations, and the R-LaTex document system using Sweave). Students in all tracks will learn how to write basic phylogenetic or comparative analysis scripts, parse NEXUS files, traverse and compute over trees, and make practical use of phylogenetic software libraries. These skills will be learned in a biological context, touching on a diverse array of topics (depending on the track) such as alignment of large numbers of sequences, ancestral state reconstruction, testing for positive selection, etc. INSTRUCTORS James Balhoff, Marguerite Butler, R. Todd Jobe, Hilmar Lapp, Darin London, David Maddison, Spencer Muse, Jeff Oliver, Brian O'Meara, William Piel, Sergei L. Kosakovsky Pond, Ryan Scherle, Todd Vision, Rutger Vos PREREQUISITES Biology: A solid understanding of phylogenetics - for example, having already taken the Workshop on Molecular Evolution (http:// www.molecularevolution.org/ ) or equivalent coursework or experience. Computing: Prior experience with Perl, Java, or R; or careful study of the suggested reading materials (see web site). Students should have experience with basic Unix shell commands. All students are expected to bring their own Mac OSX computer (a limited number of loaners are available upon request). FEES Tuition is $600.00. Accommodation is $50/night for a single occupancy apartment, $26/night for double occupancy apartment in housing provided at Duke University (students are also free to make their own housing arrangements). Travel awards of up to $450 each are available to subsidize travel expenses for applicants from underrepresented groups. HOW TO APPLY Apply through the course website (http://www.nescent.org/courses/2008/ comphy ). You will be asked to provide a resume, two references, a brief description of your computational and phylogenetic background, and your reasons for taking the course. Applications are due by April 15, 2008. International students may wish to apply for Travel Awards from the Society of Systematic Biologists (due date: March 31, 2008, see website for details). From masulli at disi.unige.it Fri Mar 28 07:34:06 2008 From: masulli at disi.unige.it (Francesco Masulli) Date: Fri, 28 Mar 2008 12:34:06 +0100 Subject: [BiO BB] CFP: CIBB 2008 3-4 October, 2008 Vietri sul Mare, Salerno (Italy) Message-ID: <200803281234.07353.masulli@disi.unige.it> Please, accept our apologies for multiple postings. ========================================================================================= CIBB 2008 FIFTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS IIASS - Vietri sul Mare, Salerno (Italy) 3-4 October, 2008 Conference Website: http://cibb08.disi.unige.it/ The main goal of the CIBB meetings is to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in bioinformatics, systems biology and medical informatics with a particular focus on Neural Networks, Machine Learning, Fuzzy Logic, and Evolutionary Computation methods. CIBB 2008 is jointly organized by: * INNS - International Neural Network Society, SIG Bioinformatics * ISCB International Society for Computational Biology * GNCS Gruppo Nazionale Calcolo Scientifico * SIREN - Italian Neural Networks Society * DISI - Univ. Genova (Italy) * DMI - Univ. Salerno (Italy) Technical areas addressed by CIBB 2008 include, but are not limited to: * Sequence analysis, promoter analysis and identification of transcription factor binding sites * Gene expression data analysis * Methods for the integration of clinical and genetic data * Algorithms for alternative splicing analysis * Methods for the functional classification of genes * Methods for the unsupervised analysis, validation and visualization of structures discovered in bio-molecular data * Prediction of secondary and tertiary protein structures * Mass spectrometry data analysis in proteomics * Methods for comparative genomics * Algorithms for molecular evolution and phylogenetic analysis * Mathematical modelling and simulation of biological systems * Heterogeneous data integration and data fusion for diagnostics * Bio-molecular databases and data mining * Algorithms for pharmacogenetics * Bio-medical text mining and imaging * Methods for diagnosis and prognosis * Software tools for bioinformatics Prof. Giuseppe Russo of Temple Univ, Philadelphia (PA-USA) has confirmed to deliver an invited talk at CIBB 2008. The scientific program will include, besides some plenary talks, contributed papers that will be presented in plenary oral or poster sessions. Accepted papers will be published in the compact disk of conference proceedings. A selection of papers presented at CIBB 2008 will be published a in post conference volume printed by an international publisher. Moreover, a selection of more relevant papers will be considered for publication in extended form in a special issue of a scientific journal we are planning. Chairs: Francesco Masulli, Universit? di Genova, Italy and Temple University, PA, USA Roberto Tagliaferri, Universit? di Salerno, Italy Gennady M. Verkhivker, University of Kansas, KS, USA, and University of California San Diego, CA, USA Scientific Program Committee: Joaquin Dopazo, Centro de Investigacion Principe Felipe, Valencia, Spain Antonio Giordano, Temple Univ, Philadelphia, PA, USA Emmanuel Ifeachor, University of Plymouth, UK Samuel Kaski, Helsinki University of Technology, Finland Natalio Krasnogor, University of Nottingham, UK Giancarlo Mauri,University of Milano Bicocca, Italy Oleg Okun, University of Oulu, Finland Giulio Pavesi, University of Milan, Italy David Alejandro Pelta, University of Granada, Spain Graziano Pesole, University of Bari, Italy Leif E. Peterson, Baylor College of Medicine Houston, TX, USA Volker Roth, ETH Zurich, Switzerland Giuseppe Russo, Temple Univ, Philadelphia, PA, USA Jean-Philippe Vert, Ecole des Mines de Paris, France (list to be updated) Steering Commitee: Pierre Baldi, University of California, Irvine, CA, USA Alexandru Floares, Oncological Institute Cluj-Napoca, Romania Jon Garibaldi, University of Nottingham, UK Francesco Masulli, University of Genova, Italy and Temple University, PA, USA Roberto Tagliaferri, University of Salerno, Italy Important Dates: Special Session Proposals: 15 May 2008 Paper submission deadline: 30 May 2008 Notification of acceptance: 30 June 2008 Final paper due: 1 September 2008 Conference: 3-4 October 2008 Special sessions: Special sessions proposals including session's title and scope, short cv of sessions chairs, preliminary list of papers (titles and authors) are due by May 15 2008. Proposals of special sessions will be evaluated as soon as they will be submitted. Please, send the proposals to cibb2008chair at disi.unige.it Paper submission: Papers must be prepared following the guidelines illustrated on the CIBB web site and cannot be longer than 10 pages. The submission of papers will be done by uploading their PDF version on the CIBB web site. =================================================== CIBB 2008 FIFTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS IIASS - Vietri sul Mare, Salerno (Italy) 3-4 October, 2008 Conference Website: http://cibb08.disi.unige.it/ email: cibb2008chair at disi.unige.it ================================================== From hlapp at gmx.net Fri Mar 28 10:38:16 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 28 Mar 2008 10:38:16 -0400 Subject: [BiO BB] Call for Student Applications - NESCent participates in the Google Summer of Code In-Reply-To: <0025B440-EF1E-4632-9DB4-B98489BF3550@duke.edu> Message-ID: <89B3A0C3-444C-40AA-B8BD-50D117B27799@gmx.net> Phyloinformatics Summer of Code 2008 http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2008 *** Please disseminate this announcement widely to appropriate students at your institution *** The National Evolutionary Synthesis Center (NESCent: http:// www.nescent.org/) is participating in 2008 for the second year as a mentoring organization in the Google Summer of Code (http:// code.google.com/soc). Through this program, Google provides undergraduate, masters, and PhD students with a unique opportunity to obtain hands-on experience writing and extending open-source software under the mentorship of experienced developers from around the world. Our goal in participating is to train future researchers and developers to not only have awareness and understanding of the value of open-source and collaboratively developed software, but also to gain the programming and remote collaboration skills needed to successfully contribute to such projects. Students will receive a stipend from Google, and may work from their home, or home institution, for the duration of the 3 month program. Students will each have one or more dedicated mentors with expertise in phylogenetic methods and open-source software development. NESCent is particularly targeting students interested in both evolutionary biology and software development. Project ideas (see URL below) range from visualizing phylogenetic data in R, to development of a Mesquite module, web-services for phylogenetic data providers or geophylogeny mashups, implementing phyloXML support, navigating databases of networks, topology queries for PhyloCode registries, to phylogenetic tree mining in a MapReduce framework, and more. The project ideas are flexible and many can be adjusted in scope to match the skills of the student. If the program sounds interesting to you but you are unsure whether you have the necessary skills, please email the mentors at the address below. We will work with you to find a project that fits your interests and skills. INQUIRIES: Email any questions, including self-proposed project ideas, to phylosoc {at} nescent {dot} org. TO APPLY: Apply on-line at the Google Summer of Code website (http://code.google.com/soc/2008), where you will also find GSoC program rules and eligibility requirements. The 1-week application period for students opened on Monday March 24th and runs through Monday, March 31st, 2008. Hilmar Lapp and Todd Vision US National Evolutionary Synthesis Center ===== URLs: ===== 2008 NESCent Phyloinformatics Summer of Code: http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2008 Eligibility requirements: http://code.google.com/opensource/gsoc/2008/faqs.html#0.1_eligibility Stipends: http://code.google.com/opensource/gsoc/2008/faqs.html#0.1_administrivia To sign up for quarterly NESCent newsletters: with announcements about upcoming programs at the Center: http://www.nescent.org/about/contact.php From idoerg at gmail.com Fri Mar 28 13:33:54 2008 From: idoerg at gmail.com (Iddo Friedberg) Date: Fri, 28 Mar 2008 10:33:54 -0700 Subject: [BiO BB] Automated Function Prediction 2008: only a few days left to submit your work! Message-ID: (Please pass on to appropriate people and lists) ONLY A FEW DAYS LEFT TO SUBMIT YOUR WORK. http://2008.BioFunctionPrediction.org/ LOCALE: Toronto, Canada (ISMB 2008) DATES: July 18-19, 2008 The Automated Function Prediction (AFP) special interest group and the Biosapiens European network of excellence are teaming up to hold a two-day Special Interest Group (SIG) meeting alongside ISMB 2008. The deluge of genomic information is challenging biologists to annotate this data, from locating genes in the raw data through predicting the function form protein sequence and structure. AFP and Biosapiens share many common goals, and this year we have decided to join forces for a meeting that will deal with a wide scope of gene, protein, and genomic annotations. This meeting is held alongside ISMB, the largest conference on computational biology worldwide. This year we are also considering mini-tutorial submissions. Please see the AFP / Biosapiens site for more information. http://2008 .BioFunctionPrediction.org/ IMPORTANT DATES: Talk, tutorial and poster abstracts due: March 31, 2008 Notification of acceptance: April 20, 2008 Final abstracts due: May 5, 2008 AFP-Biosapiens SIG : July 18-19, 2008 Confirmed keynote speakers include: - Patricia Babbitt, University of California San Francisco, USA - Peer Bork, European Molecular Biology Laboratories, Germany - Andrew Emili, University of Toronto, Canada - Roderic Guig?, Institut Municipal d'Investigaci? M?dica, Universitat Pompeu Fabra, Spain - Barry Honig, Columbia University and Howard Hughes Medical Institute, USA - Kimmen Sj?lander, University of California Berkeley, USA - Olga Troyanskaya, Princeton University, USA FOR MORE INFORMATION: http://2008.BioFunctionPrediction.org/ About ISMB 2008: http://www.iscb.org/ismb2008/ For inquiries, including sponsorship opportunities, please email: afpbiosap2008 at gmail.com -- Iddo Friedberg, Ph.D. CALIT2, mail code 0440 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0440, USA T: +1 (858) 534-0570 T: +1 (858) 646-3100 x3516 http://iddo-friedberg.org From idoerg at gmail.com Fri Mar 28 21:08:10 2008 From: idoerg at gmail.com (Iddo Friedberg) Date: Fri, 28 Mar 2008 18:08:10 -0700 Subject: [BiO BB] Last call for abstracts: Automated Function Prediction / Biosapiens 2008 Message-ID: (Please pass on to appropriate people and lists. Apologies if you receive this more than once) ONLY A FEW DAYS LEFT TO SUBMIT YOUR WORK. LOCALE: Toronto, Canada (ISMB 2008) DATES: July 18-19, 2008 The Automated Function Prediction (AFP) special interest group and the Biosapiens European network of excellence are teaming up to hold a two-day Special Interest Group (SIG) meeting alongside ISMB 2008. The deluge of genomic information is challenging biologists to annotate this data, from locating genes in the raw data through predicting the function form protein sequence and structure. AFP and Biosapiens share many common goals, and this year we have decided to join forces for a meeting that will deal with a wide scope of gene, protein, and genomic annotations. This meeting is held alongside ISMB, the largest conference on computational biology worldwide. This year we are also considering mini-tutorial submissions. Please see the AFP / Biosapiens site for more information. IMPORTANT DATES: Talk, tutorial and poster abstracts due: March 31, 2008 Notification of acceptance: April 20, 2008 Final abstracts due: May 5, 2008 AFP-Biosapiens SIG : July 18-19, 2008 Confirmed keynote speakers include: - Patricia Babbitt, University of California San Francisco, USA - Peer Bork, European Molecular Biology Laboratories, Germany - Andrew Emili, University of Toronto, Canada - Roderic Guig?, Institut Municipal d'Investigaci? M?dica, Universitat Pompeu Fabra, Spain - Barry Honig, Columbia University and Howard Hughes Medical Institute, USA - Kimmen Sj?lander, University of California Berkeley, USA - Olga Troyanskaya, Princeton University, USA FOR MORE INFORMATION: http://2008.BioFunctionPrediction.org/< http://2008.biofunctionprediction.org/> About ISMB 2008: http://www.iscb.org/ismb2008/ For inquiries, including sponsorship opportunities, please email: afpbiosap2008 at gmail.com -- Iddo Friedberg, Ph.D. CALIT2, mail code 0440 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0440, USA T: +1 (858) 534-0570 T: +1 (858) 646-3100 x3516 http://iddo-friedberg.org From markii at came.sbg.ac.at Mon Mar 31 04:21:18 2008 From: markii at came.sbg.ac.at (Markus Wiederstein) Date: Mon, 31 Mar 2008 10:21:18 +0200 Subject: [BiO BB] TopMatch protein structure alignment and superposition web service Message-ID: <20080331082118.GF31003@came.sbg.ac.at> We announce the release of TopMatch-web, a public web service for the alignment and superposition of protein structures and the instant +visualization of structural similiarities. We believe that TopMatch is an exceptionally effective, accurate, and enjoyable program for the investigation of protein structure similarities. For further information and instructive examples see Sippl & Wiederstein (2008) A Note on Difficult Structure Alignment Problems. Bioinformatics 24, pp. 426-427 TopMatch-web is available as a public web service at http://topmatch.services.came.sbg.ac.at. Enjoy! The TopMatch Team Center of Applied Molecular Engineering University of Salzburg Austria From mtong at seralogix.com Mon Mar 31 14:30:42 2008 From: mtong at seralogix.com (Mark Tong) Date: Mon, 31 Mar 2008 13:30:42 -0500 Subject: [BiO BB] hOW TO LINK TRANSCRIPTION FACTOR TO ITS REGULATED GENES? Message-ID: <001a01c8935d$53db9440$bd0211ac@sanger> Can any one help me with a database/web site that links known transcription factor with its regulated genes? Thanks in advance, Mark From Sterten at aol.com Mon Mar 31 16:35:07 2008 From: Sterten at aol.com (Sterten at aol.com) Date: Mon, 31 Mar 2008 16:35:07 EDT Subject: [BiO BB] TopMatch protein structure alignment and superposition web service Message-ID: is it faster or better than MAFFT, which I use currently ? http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ From jeff at bioinformatics.org Mon Mar 31 17:14:35 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 31 Mar 2008 17:14:35 -0400 Subject: [BiO BB] March '08 issue of the Bioinformatics.Org Newsletter is now available Message-ID: <47F1543B.2030504@bioinformatics.org> The newsletter includes some of the best of our various online forums and details some of our internal (and external) activities. IN THIS ISSUE: - Unveiling Pipet (part two) - Project spotlight: Molekel - Job search highlight - Upcoming events URL: http://www.bioinformatics.org/newsletter/v01-n03.pdf Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 562 4800 -- From marchywka at hotmail.com Mon Mar 31 20:43:41 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 31 Mar 2008 20:43:41 -0400 Subject: [BiO BB] TopMatch protein structure alignment and superposition web service In-Reply-To: References: Message-ID: I've used the Protein3dfit link from here , http://biotool.uni-koeln.de but it seems to be down right now. One suggestion I would make, however, is to offer an API and not just a web interface. I have a script to use the above link so I can submit files from a command line ( and integrate into automated stuff) and I imagine your form could be reverse engineered too. Trying to reverse engineer html is always annoying and it would probably be easier for you to write your web pages on top of a documented stable API. Whlie the interactive java viwer may not make much sense in this usage situation, your do offer pdf and pdb downloads that could be automated- if there is really something in the pdf that is not in the pdb, text format may be easier although certainly the pdb file is quite usable for automated analysis. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on marchywka at yahoo.com if no reply here. Thanks. > From: Sterten at aol.com > Date: Mon, 31 Mar 2008 16:35:07 -0400 > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] TopMatch protein structure alignment and superposition web service > > is it faster or better than MAFFT, which I use currently ? > http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ > > > > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ How well do you know your celebrity gossip? http://originals.msn.com/thebigdebate?ocid=T002MSN03N0707A From ahmed.essaghir at gmail.com Mon Mar 31 18:14:58 2008 From: ahmed.essaghir at gmail.com (ahmed essaghir) Date: Tue, 1 Apr 2008 00:14:58 +0200 Subject: [BiO BB] hOW TO LINK TRANSCRIPTION FACTOR TO ITS REGULATED GENES? In-Reply-To: <001a01c8935d$53db9440$bd0211ac@sanger> References: <001a01c8935d$53db9440$bd0211ac@sanger> Message-ID: <6ec4c2000803311514o5003bbe1l8fa6c08ed6633183@mail.gmail.com> try this : TRED database http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home On Mon, Mar 31, 2008 at 8:30 PM, Mark Tong wrote: > Can any one help me with a database/web site that links known > transcription factor with its regulated genes? > > Thanks in advance, > > Mark > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb >