From vijayendran_vijay at hotmail.com Wed May 5 06:48:00 2004 From: vijayendran_vijay at hotmail.com (Chandran Vijayendran) Date: Wed, 05 May 2004 10:48:00 +0000 Subject: [BiO BB] E.coli strain differences Message-ID: Dear all, I would like to compare the whole genome of two E.coli strains, (K12-MG-1655 and K12 W3110). Where MG strain genome is available at NCBI and W3110 strain genome is available at Genobase. I would like to know gene arrangement differences in both the strain. Is this data is already available on net? If not how shall I proceed on? Thanks for your time, -Vijay- ?????????????????????????????????????????? Chandran Vijayendran, PhD Student, Graduate school in Bioinformatics and Genome research. c/o Prof. Erwin Flaschel,D5-120. Technical faculty, University of Bielefeld,Universitaets str -25,D-33615,Bielefeld. Germany. Phone Home: + 49 (0)521-3279769. Off: + 49 (0)521-1065286. Mobile: + 49 (0)17624024791. ?????????????????????????????????????????? _________________________________________________________________ Contact brides & grooms FREE! http://www.shaadi.com/ptnr.php?ptnr=hmltag Only on www.shaadi.com. Register now! From wwhsiao at sfu.ca Wed May 5 13:54:40 2004 From: wwhsiao at sfu.ca (William Hsiao) Date: Wed, 5 May 2004 10:54:40 -0700 Subject: [BiO BB] RE: E.coli strain differences (Chandran Vijayendran) In-Reply-To: <20040505160107.22347D1F0D@www.bioinformatics.org> Message-ID: <000c01c432ca$0fdeaa90$a50aa8c0@microbe> I think you can use MUMmer (http://www.tigr.org/software/mummer/) to align the two genomes and extract regions in W3110 that do not align with MG-1655. Since MUMmer (specifically NUCmer) produces a linear alignment, gene rearrangements show up as alignments off the x=y diagonal and additional genes show up as gaps. You can extract sequences from off-centered alignments and gaps, and perform BLAST analysis to find out the gene content (or if the genomes are annotated, read them off an annotation file such as .ptt files from NCBI). Cheers Will William Hsiao PhD Student, Brinkman Laboratory Department of Molecular Biology and Biochemistry Simon Fraser University, 8888 University Dr. Burnaby, BC, Canada V5A 1S6 Phone: 604-291-4206 Fax: 604-291-5583 -----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: May 5, 2004 9:01 AM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #679 - 1 msg 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. E.coli strain differences (Chandran Vijayendran) --__--__-- Message: 1 From: "Chandran Vijayendran" To: bio_bulletin_board at bioinformatics.org Date: Wed, 05 May 2004 10:48:00 +0000 Subject: [BiO BB] E.coli strain differences Reply-To: bio_bulletin_board at bioinformatics.org Dear all, I would like to compare the whole genome of two E.coli strains, (K12-MG-1655 and K12 W3110). Where MG strain genome is available at NCBI and W3110 strain genome is available at Genobase. I would like to know gene arrangement differences in both the strain. Is this data is already available on net? If not how shall I proceed on? Thanks for your time, -Vijay- ?????????????????????????????????????????? Chandran Vijayendran, PhD Student, Graduate school in Bioinformatics and Genome research. c/o Prof. Erwin Flaschel,D5-120. Technical faculty, University of Bielefeld,Universitaets str -25,D-33615,Bielefeld. Germany. Phone Home: + 49 (0)521-3279769. Off: + 49 (0)521-1065286. Mobile: + 49 (0)17624024791. ?????????????????????????????????????????? _________________________________________________________________ Contact brides & grooms FREE! http://www.shaadi.com/ptnr.php?ptnr=hmltag Only on www.shaadi.com. Register now! --__--__-- _______________________________________________ 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 j.d.tucker at vla.defra.gsi.gov.uk Thu May 6 04:01:48 2004 From: j.d.tucker at vla.defra.gsi.gov.uk (Tucker, James) Date: Thu, 6 May 2004 09:01:48 +0100 Subject: [BiO BB] E.coli comparison Message-ID: <104FE795DA19D411A71A0008C733F76404A43C8A@vla6.wyr.maff.gov.uk> Hi Vijay, The Sanger centre - has ACT (Artemis Comparison Tool) available for Just this kind of thing. It is freely available and you can download it onto your PC/Mac. It is very easy to use and gives you a visual output of the similarities/differences in the genomes. Hope this helps Regards James Today's Topics: 1. E.coli strain differences (Chandran Vijayendran) --__--__-- Message: 1 From: "Chandran Vijayendran" To: bio_bulletin_board at bioinformatics.org Date: Wed, 05 May 2004 10:48:00 +0000 Subject: [BiO BB] E.coli strain differences Reply-To: bio_bulletin_board at bioinformatics.org Dear all, I would like to compare the whole genome of two E.coli strains, (K12-MG-1655 and K12 W3110). Where MG strain genome is available at NCBI and W3110 strain genome is available at Genobase. I would like to know gene arrangement differences in both the strain. Is this data is already available on net? If not how shall I proceed on? Thanks for your time, -Vijay- ?????????????????????????????????????????? Chandran Vijayendran, PhD Student, Graduate school in Bioinformatics and Genome research. c/o Prof. Erwin Flaschel,D5-120. Technical faculty, University of Bielefeld,Universitaets str -25,D-33615,Bielefeld. Germany. Phone Home: + 49 (0)521-3279769. Off: + 49 (0)521-1065286. Mobile: + 49 (0)17624024791. ?????????????????????????????????????????? _________________________________________________________________ Contact brides & grooms FREE! http://www.shaadi.com/ptnr.php?ptnr=hmltag Only on www.shaadi.com. Register now! --__--__-- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest 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. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3950 bytes Desc: not available URL: From roy at colibase.bham.ac.uk Thu May 6 13:48:44 2004 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Thu, 06 May 2004 18:48:44 +0100 Subject: [BiO BB] RE: E.coli strain differences Message-ID: <409A7A7C.6030100@colibase.bham.ac.uk> > I would like to compare the whole genome of two E.coli strains, > (K12-MG-1655 and K12 W3110). Where MG strain genome is available at > NCBI and W3110 strain genome is=20 available at Genobase. I would > like to know gene arrangement differences in both the strain. Is this > data is already available on net? If not how shall I proceed on? Our database coliBASE (http://colibase.bham.ac.uk) is a comparative genomics database for analysis of E.coli and its relatives. It includes precalculated MUMmer (and PROmer) alignments and has a built in user-friendly online display tool, to save you the bother of downloading ACT. The database includes K12 MG1655 and W3110, as well many other genomes. This link: http://colibase.bham.ac.uk/cgi-bin/viewgenome.cgi?accession=U00096&scheme=ortho&frame=genome&help=genomechoose&palette=gr&genome=ECO_W3110 shows a whole genome view of K12 MG1655, with the genes coloured in according to the presence or absence of orthologues in W3110 (genes with no annotated orthologue are coloured in red). From this global view it's easy to identify regions of difference, and these can be viewed in detail by clicking on them. For example: http://colibase.bham.ac.uk/cgi-bin/contigalignment.cgi?accession=U00096&start=2549822&end=2569821&display=arrow&scale=33&alnacc=ECO_W3110 this link shows one of the (very few) regions of difference between the two strains, with an insertion in MG1655 that is absent from W3110, highlighted using MUMmer. A description of coliBASE was published in the NAR database issue which is freely available on the web: http://nar.oupjournals.org/cgi/content/abstract/32/suppl_1/D296 Oh, and sorry for the blatant advertising, but if anyone's interested we have similar databases for Pseudomonas (http://pseudo.bham.ac.uk), Campylobacter and related genera (http://campy.bham.ac.uk) and Clostridium (http://clostri.bham.ac.uk). Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow, Division of Immunity and Infection, University of Birmingham, UK http://colibase.bham.ac.uk From stefanielager at fastmail.ca Fri May 7 01:56:24 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Fri, 7 May 2004 05:56:24 +0000 (UTC) Subject: [BiO BB] Graphical dispaly of secondary structure Message-ID: <20040507055625.5284186577E@mail.interchange.ca> Hi, I'm looking for a program that can graphically display secondary structure of protein sequences (alpha helix, beta strand, coil). I've seen these multiple alignments with secondary structures displayed graphically below, but I would like to use it with predicted secondary structures. But I can't find any program that can display multiple alignments with graphical display of the secondary structure. Stfeanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From praseetha at eth.net Fri May 7 21:33:49 2004 From: praseetha at eth.net (praseetha) Date: Sat, 8 May 2004 07:03:49 +0530 Subject: [BiO BB] msc project in bioinformatics Message-ID: <001101c4349c$a65446a0$6da809ca@praseeth> Respected sir i am doing my msc in bioinformatics at periyar university.i shall be highly obliged if you would kindly provide me with necessary information to do my project in banglore or madras during december2004-march2005. -------------- next part -------------- An HTML attachment was scrubbed... URL: From risea at cecalc.ula.ve Tue May 11 16:08:07 2004 From: risea at cecalc.ula.ve (Raul Isea) Date: Tue, 11 May 2004 16:08:07 -0400 (VET) Subject: [BiO BB] Course: Introduction to Molecular Epidemiology in Merida - Message-ID: <3938.150.185.138.94.1084306087.squirrel@topca.ula.ve> Event: Introduction to Molecular Epidemiology Merida Venezuela July 12-17, 2004 Objective: To provide analytical tools for molecular data interpretation in the context of epidemologic research. Speakers: Dr. Marcelo Briones Universidade Federal de S?o Paulo, Brazil Dr. Ananias A. Escalante Centro de Ecolog?a, Instituto Venezolano de Investigaciones Cient?ficas Dr. Marcelo Urbano Ferreira Department of Parasitology, Institute for Biomedical Sciences, University of S?o Paulo, Brazil Dr. Fernando Monteiro Laborat?rio de Doen?as Parasit?rias, Departamento de Medicina Tropical, Instituto Oswaldo Cruz, Brazil Dr. Lyda Osorio Centro Internacional de Entrenamiento e Investigaciones M?dicas, Cali, COLOMBIA Dr. Valeria Souza Laboratorio de Evoluci?n Molecular y Experimental, Dept. de Ecolog?a Evolutiva, Instituto de Ecolog?a, UNAM, Mexico Dr. Ludmel Urdaneta Centro de Investigaciones Biom?dicas, BIOMED. Universidad de Carabobo, Venezuela. Program: * Basic Concepts in Epidemiology: using molecular markers (Lyda Osorio) * Techniques for assessing genetic variation: an overview (Ludmel Urdaneta) * Basic concepts in population genetics (Ananias Escalante) * Recombination and Linkage Disequilibrium (Marcelo Ferreira) * Population Structure (Valeria Souza) * Molecular Systematic methods: an overview (Marcelo Briones) * Molecular epidemiology and medical entomology (Fernando Monteiro) Participants Profile: * All participants must speak and understand English. * All participants must master basic concepts in statistics and genetics. * All participants should be interested in epidemiologic investigations. * Basic computer skills are desirable but they will be provided. * Basic knowledge in laboratory techniques is desirable (RAPDs, RFLP, sequencing). Sponsored by: *UNU/Biolac (United Nations University / Biotechnology for Latin America and The Caribbean). *Latin American Network in Molecular Epidemiology (LANMEp) *Centers for Disease Control and Prevention. *Instituto Venezolano de Investigaciones Cient?ficas. *Universidad de Los Andes (ULA). *Centro Nacional de C?lculo Cient?fico (CeCalCULA). More Information: Centro Nacional de Calculo Cient?fico Universidad de los Andes, Centro Profesional Masini, Av.4 entre calles 18 y 19, Piso 3, Ofic. B-32, M?rida 5101, Venezuela Tel. +58-274-22524192 fax: +58-274-2525473 E-mail: bioinfo at cecalc.ula.ve **** Dr. Raul Isea PhD in Chemistry Email: risea at cecalc.ula.ve http://www.cecalc.ula.ve/~risea (Mirror at http://www.geocities.com/lrisea) Fax in USA : 1(208)978-2122 Fax in Venezuela: 58 (274) 2525473 From letondal at pasteur.fr Thu May 13 07:55:51 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Thu, 13 May 2004 13:55:51 +0200 Subject: [BiO BB] Graphical dispaly of secondary structure In-Reply-To: Your message of "Fri, 07 May 2004 05:56:24 -0000." <20040507055625.5284186577E@mail.interchange.ca> Message-ID: <200405131155.i4DBtqqf258040@electre.pasteur.fr> "Stefanie Lager" wrote: > Hi, > > I'm looking for a program that can graphically display secondary > structure of protein sequences (alpha helix, beta strand, coil). I've > seen these multiple alignments with secondary structures displayed > graphically below, but I would like to use it with predicted secondary > structures. But I can't find any program that can display multiple > alignments with graphical display of the secondary structure. > > Stfeanie You can look here: http://bioweb.pasteur.fr/cgi-bin/seqanal/review-edital.pl -- Catherine Letondal -- Pasteur Institute Computing Center From deletto at unisa.it Fri May 14 07:03:40 2004 From: deletto at unisa.it (deletto at unisa.it) Date: Fri, 14 May 2004 13:03:40 +0200 Subject: [BiO BB] howto convert affym gene ID into MOD system Message-ID: <1084532620.40a4a78c5cd0f@webmail.unisa.it> Dear all, I would like to know whether there are free softwares for converting affymetrix gene ID into MOD (Model Organism Database) system. thanks in advance davide ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From dmb at mrc-dunn.cam.ac.uk Fri May 14 09:10:08 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 14 May 2004 14:10:08 +0100 (BST) Subject: [BiO BB] GeneBank to SwissProt Mapping? Message-ID: Any body know how to map proteins from the NCBI to proteins from the EBI? Cheers, Dan. From B.A.T.Svensson at lumc.nl Fri May 14 09:07:12 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: 14 May 2004 15:07:12 +0200 Subject: [BiO BB] GeneBank to SwissProt Mapping? In-Reply-To: References: Message-ID: <1084540031.6516.37.camel@ander> What data do you have to start with? On Fri, 2004-05-14 at 15:10, Dan Bolser wrote: > Any body know how to map proteins from the NCBI to proteins from the EBI? > > Cheers, > Dan. From dmb at mrc-dunn.cam.ac.uk Fri May 14 09:28:57 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 14 May 2004 14:28:57 +0100 (BST) Subject: [BiO BB] GeneBank to SwissProt Mapping? In-Reply-To: <1084540031.6516.37.camel@ander> Message-ID: On 14 May 2004, Svensson, B.A.T. (HKG) wrote: >What data do you have to start with? BIND.... I am thinking that blast will get the job done if I use refseq... > > >On Fri, 2004-05-14 at 15:10, Dan Bolser wrote: >> Any body know how to map proteins from the NCBI to proteins from the EBI? >> >> Cheers, >> Dan. > >_______________________________________________ >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 Fri May 14 10:16:11 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: 14 May 2004 16:16:11 +0200 Subject: [BiO BB] GeneBank to SwissProt Mapping? In-Reply-To: References: Message-ID: <1084544171.6516.47.camel@ander> On Fri, 2004-05-14 at 15:28, Dan Bolser wrote: > On 14 May 2004, Svensson, B.A.T. (HKG) wrote: > > >What data do you have to start with? > > BIND.... I am thinking that blast will get the job done if I use refseq... I don't know about BIND, but if you have refseq, then you will be able to fetch the protein identifier (PID) as well as well as the official gene symbol from NCBI's data set UniGene (pre-blasted as to say), this should be enough to link to your data. If you need help with retrieving PID's and gene symbols, let me know and I can make a query in my own database to retrieve this data for you - or anything else you need from UniGene. Precisely which EBI dataset would you like to link to? > >On Fri, 2004-05-14 at 15:10, Dan Bolser wrote: > >> Any body know how to map proteins from the NCBI to proteins from the EBI? > >> > >> Cheers, > >> Dan. > > From pculpep at hotmail.com Fri May 14 11:52:39 2004 From: pculpep at hotmail.com (Pamela Culpepper) Date: Fri, 14 May 2004 15:52:39 +0000 Subject: [BiO BB] GeneBank to SwissProt Mapping? Message-ID: Another place to look -- www.geneontgology.org/GO.indicies.html. These files have lots of cross-references. Pam >From: "Svensson, B.A.T. (HKG)" >Reply-To: bio_bulletin_board at bioinformatics.org >To: Bio Bulletin >Subject: Re: [BiO BB] GeneBank to SwissProt Mapping? >Date: 14 May 2004 15:07:12 +0200 > >What data do you have to start with? > > >On Fri, 2004-05-14 at 15:10, Dan Bolser wrote: > > Any body know how to map proteins from the NCBI to proteins from the >EBI? > > > > Cheers, > > Dan. > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From pculpep at hotmail.com Fri May 14 11:59:38 2004 From: pculpep at hotmail.com (Pamela Culpepper) Date: Fri, 14 May 2004 15:59:38 +0000 Subject: [BiO BB] GeneBank to SwissProt Mapping? Message-ID: Also, grab the LL_tmpl.gz from the refseq/LocusLink directory at ftp.ncbi.nih.gov. This file comprises the LocusLink template pages. Lots of info there, too. Pam >From: "Svensson, B.A.T. (HKG)" >Reply-To: bio_bulletin_board at bioinformatics.org >To: Bio Bulletin >Subject: Re: [BiO BB] GeneBank to SwissProt Mapping? >Date: 14 May 2004 16:16:11 +0200 > > > > >On Fri, 2004-05-14 at 15:28, Dan Bolser wrote: > > On 14 May 2004, Svensson, B.A.T. (HKG) wrote: > > > > >What data do you have to start with? > > > > BIND.... I am thinking that blast will get the job done if I use >refseq... > >I don't know about BIND, but if you have refseq, then you will be able >to fetch the protein identifier (PID) as well as well as the official >gene symbol from NCBI's data set UniGene (pre-blasted as to say), this >should be enough to link to your data. If you need help with retrieving >PID's and gene symbols, let me know and I can make a query in my own >database to retrieve this data for you - or anything else you need from >UniGene. > >Precisely which EBI dataset would you like to link to? > > > > >On Fri, 2004-05-14 at 15:10, Dan Bolser wrote: > > >> Any body know how to map proteins from the NCBI to proteins from the >EBI? > > >> > > >> Cheers, > > >> Dan. > > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From pculpep at hotmail.com Fri May 14 12:11:21 2004 From: pculpep at hotmail.com (Pamela Culpepper) Date: Fri, 14 May 2004 16:11:21 +0000 Subject: [BiO BB] howto convert affym gene ID into MOD system Message-ID: Try -- www.genmapp.org/ Pam >From: deletto at unisa.it >Reply-To: bio_bulletin_board at bioinformatics.org >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] howto convert affym gene ID into MOD system >Date: Fri, 14 May 2004 13:03:40 +0200 > > > >Dear all, >I would like to know whether there are free softwares for converting >affymetrix >gene ID into MOD (Model Organism Database) system. > >thanks in advance > >davide > >------------------------------------------------- >This mail sent through IMP: http://horde.org/imp/ >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jhao at tgen.org Fri May 14 16:44:47 2004 From: jhao at tgen.org (Jicheng Hao) Date: Fri, 14 May 2004 13:44:47 -0700 Subject: [BiO BB] characterization of an incomplete genome Message-ID: <8C5AFD8EFC7B1A4EA246BA5BB1BAAE4F108D13@TGEN-M1.ad.tgen.org> Hi there, We have assembled a Yesinia pestis genome. However, the genome is only 95% complete. We would like to to characterize rearrangements, large, medium size indels, repeat differences, gene differences by comparing it with a known complete genome. I would appreciate if anybody could give me any advice or comments. Jicheng Hao, Ph.D. Staff Scientist, Bioinformatics Comparative Genomics Unit Pathogen Genomics Division Translational Genomics Research Institute (TGen) 602 343 8705 (phone) 480 570 5969 (mobile) 602 343 8740 (fax) jhao at tgen.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From ryangolhar at hotmail.com Fri May 14 20:30:29 2004 From: ryangolhar at hotmail.com (Ryan Golhar) Date: Fri, 14 May 2004 20:30:29 -0400 Subject: [BiO BB] characterization of an incomplete genome In-Reply-To: <8C5AFD8EFC7B1A4EA246BA5BB1BAAE4F108D13@TGEN-M1.ad.tgen.org> Message-ID: <000801c43a13$d33c98d0$1300a8c0@GOLHARMOBILE1> First thing I would do is obtain the genome of another organism related to Yesinia pestis that is annotated and compare the two genomes as a starting point. ----- Ryan Golhar Computational Biologist 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: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Jicheng Hao Sent: Friday, May 14, 2004 4:45 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] characterization of an incomplete genome Hi there, We have assembled a Yesinia pestis genome. However, the genome is only 95% complete. We would like to to characterize rearrangements, large, medium size indels, repeat differences, gene differences by comparing it with a known complete genome. I would appreciate if anybody could give me any advice or comments. Jicheng Hao, Ph.D. Staff Scientist, Bioinformatics Comparative Genomics Unit Pathogen Genomics Division Translational Genomics Research Institute (TGen) 602 343 8705 (phone) 480 570 5969 (mobile) 602 343 8740 (fax) jhao at tgen.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Sat May 15 05:35:00 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat, 15 May 2004 10:35:00 +0100 (BST) Subject: [BiO BB] GeneBank to SwissProt Mapping? In-Reply-To: <1084544171.6516.47.camel@ander> Message-ID: Thanks Pamela for your suggestions, I have tried LocusLink (the 'loc2acc' file) but I find many missing swissprot / trembl accession numbers. I fear that the GO mapping could be incomplete for other resons too. Thanks Svensson for the offer of assistance below, but I am not sure how having PID will help me. (sorry for my ignorance). I know sptrembl has a good PIR mapping, can we get to PIR from GI? I am running blast jobs at the minuite as the bind sequence file isn't too big, but getting accurate 1-1 mapping means that I have to blast against the full datasets and not some non redundant version thereof. 4 more days to go... If anyone wants the data let me know. Dan. On 14 May 2004, Svensson, B.A.T. (HKG) wrote: > > > >On Fri, 2004-05-14 at 15:28, Dan Bolser wrote: >> On 14 May 2004, Svensson, B.A.T. (HKG) wrote: >> >> >What data do you have to start with? >> >> BIND.... I am thinking that blast will get the job done if I use refseq... > >I don't know about BIND, but if you have refseq, then you will be able >to fetch the protein identifier (PID) as well as well as the official >gene symbol from NCBI's data set UniGene (pre-blasted as to say), this >should be enough to link to your data. If you need help with retrieving >PID's and gene symbols, let me know and I can make a query in my own >database to retrieve this data for you - or anything else you need from >UniGene. > >Precisely which EBI dataset would you like to link to? > > >> >On Fri, 2004-05-14 at 15:10, Dan Bolser wrote: >> >> Any body know how to map proteins from the NCBI to proteins from the EBI? >> >> >> >> Cheers, >> >> Dan. >> > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From anand.kumar at ifomis.uni-leipzig.de Sat May 15 06:09:35 2004 From: anand.kumar at ifomis.uni-leipzig.de (Anand Kumar) Date: Sat, 15 May 2004 12:09:35 +0200 (CEST) Subject: [BiO BB] GeneBank to SwissProt Mapping? References: Message-ID: <5147886.1084615775343.SLOX.WebMail.wwwrun@hogwarts.imise.uni-leipzig.de> Dan, We, with the Swissprot team, have begun to work in the area of bridging the gap between disease and gene products as a pilot project. This would help to bridge the gap between diseases and gene products, as it exists in OMIM. We are trying to address various granularities from clinical to molecular levels. Are you doing the mapping for human proteins? That could help us since we already use the annotations present with GO to the respective gene products. Kind Regards, Anand. Am Sa 15.05.2004 11:35, Dan Bolser schrieb: > > Thanks Pamela for your suggestions, I have tried LocusLink (the 'loc2acc' > file) but I find many missing swissprot / trembl accession numbers. I > fear that the GO mapping could be incomplete for other resons too. > > Thanks Svensson for the offer of assistance below, but I am not sure how > having PID will help me. (sorry for my ignorance). > > I know sptrembl has a good PIR mapping, can we get to PIR from GI? > > I am running blast jobs at the minuite as the bind sequence file isn't too > big, but getting accurate 1-1 mapping means that I have to blast against > the full datasets and not some non redundant version thereof. > > 4 more days to go... > > If anyone wants the data let me know. > > Dan. > > > > On 14 May 2004, Svensson, B.A.T. (HKG) wrote: > > > > > > > > >On Fri, 2004-05-14 at 15:28, Dan Bolser wrote: > >> On 14 May 2004, Svensson, B.A.T. (HKG) wrote: > >> > >> >What data do you have to start with? > >> > >> BIND.... I am thinking that blast will get the job done if I use refseq... > > > >I don't know about BIND, but if you have refseq, then you will be able > >to fetch the protein identifier (PID) as well as well as the official > >gene symbol from NCBI's data set UniGene (pre-blasted as to say), this > >should be enough to link to your data. If you need help with retrieving > >PID's and gene symbols, let me know and I can make a query in my own > >database to retrieve this data for you - or anything else you need from > >UniGene. > > > >Precisely which EBI dataset would you like to link to? > > > > > >> >On Fri, 2004-05-14 at 15:10, Dan Bolser wrote: > >> >> Any body know how to map proteins from the NCBI to proteins from the EBI? > >> >> > >> >> Cheers, > >> >> Dan. > >> > > >_______________________________________________ > >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 > Anand Kumar MBBS, PhD IFOMIS Faculty of Medicine University of Leipzig H?rtelstra?e 16-18 04107 Leipzig Germany http://www.uni-leipzig.de/~akumar/ From dmb at mrc-dunn.cam.ac.uk Sat May 15 06:38:54 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat, 15 May 2004 11:38:54 +0100 (BST) Subject: [BiO BB] GeneBank to SwissProt Mapping? In-Reply-To: <5147886.1084615775343.SLOX.WebMail.wwwrun@hogwarts.imise.uni-leipzig.de> Message-ID: On Sat, 15 May 2004, Anand Kumar wrote: >Dan, > >We, with the Swissprot team, have begun to work in the area of bridging >the gap between disease and gene products as a pilot project. This would >help to bridge the gap between diseases and gene products, as it exists >in OMIM. We are trying to address various granularities from clinical to >molecular levels. Are you doing the mapping for human proteins? That >could help us since we already use the annotations present with GO to >the respective gene products. To clarify what I am doing: I take BIND protein interaction data, and for each sequence available in bind (with a GI accession number) I blast against SPTrEMBL. This data will give me a GI <-> SP accession number mapping for the dataset I am interested in. It will also create (as a side effect) a whole load of data about close homologues of the protein sequences available in BIND, which could be very useful. It will be easy to make a human subset of the data, for example http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15117749&dopt=Abstract Please let me know, Dan. > >Kind Regards, >Anand. > >Am Sa 15.05.2004 11:35, Dan Bolser schrieb: > >> >> Thanks Pamela for your suggestions, I have tried LocusLink (the 'loc2acc' >> file) but I find many missing swissprot / trembl accession numbers. I >> fear that the GO mapping could be incomplete for other resons too. >> >> Thanks Svensson for the offer of assistance below, but I am not sure how >> having PID will help me. (sorry for my ignorance). >> >> I know sptrembl has a good PIR mapping, can we get to PIR from GI? >> >> I am running blast jobs at the minuite as the bind sequence file isn't too >> big, but getting accurate 1-1 mapping means that I have to blast against >> the full datasets and not some non redundant version thereof. >> >> 4 more days to go... >> >> If anyone wants the data let me know. >> >> Dan. >> >> >> >> On 14 May 2004, Svensson, B.A.T. (HKG) wrote: >> >> > >> > >> > >> >On Fri, 2004-05-14 at 15:28, Dan Bolser wrote: >> >> On 14 May 2004, Svensson, B.A.T. (HKG) wrote: >> >> >> >> >What data do you have to start with? >> >> >> >> BIND.... I am thinking that blast will get the job done if I use refseq... >> > >> >I don't know about BIND, but if you have refseq, then you will be able >> >to fetch the protein identifier (PID) as well as well as the official >> >gene symbol from NCBI's data set UniGene (pre-blasted as to say), this >> >should be enough to link to your data. If you need help with retrieving >> >PID's and gene symbols, let me know and I can make a query in my own >> >database to retrieve this data for you - or anything else you need from >> >UniGene. >> > >> >Precisely which EBI dataset would you like to link to? >> > >> > >> >> >On Fri, 2004-05-14 at 15:10, Dan Bolser wrote: >> >> >> Any body know how to map proteins from the NCBI to proteins from the EBI? >> >> >> >> >> >> Cheers, >> >> >> Dan. >> >> > >> >_______________________________________________ >> >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 >> > >Anand Kumar MBBS, PhD >IFOMIS >Faculty of Medicine >University of Leipzig >H??rtelstra??e 16-18 >04107 Leipzig >Germany >http://www.uni-leipzig.de/~akumar/ > > > > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From anand.kumar at ifomis.uni-leipzig.de Sat May 15 07:28:12 2004 From: anand.kumar at ifomis.uni-leipzig.de (Anand Kumar) Date: Sat, 15 May 2004 13:28:12 +0200 (CEST) Subject: [BiO BB] GeneBank to SwissProt Mapping? References: Message-ID: <2094134.1084620492070.SLOX.WebMail.wwwrun@hogwarts.imise.uni-leipzig.de> Dan, > > To clarify what I am doing: > > I take BIND protein interaction data, and for each sequence available in > bind (with a GI accession number) I blast against SPTrEMBL. This data will > give me a GI <-> SP accession number mapping for the dataset I am > interested in. > > It will also create (as a side effect) a whole load of data about close > homologues of the protein sequences available in BIND, which could be very > useful. > > It will be easy to make a human subset of the data, for example > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15117749&dopt=Abstract Thanks for your prompt reply. Yes it would be very useful to have this data. Since we already have the Uniprot id of human proteins, in which we are interested (and of course their names), it would be nice to know about their interactions with other human proteins. We have a set of ontologies which goes from the disease level to the cellular and subcellular level and this data will fit well with the lower level of granularity. Our end goal is to find the collaborations by which we wouldbe able to make a full-fledged carcinoma server, where various carcinoma related information can be searched from the name of disease, organ, drug, symptom, protein, cell, gene etc. Kind Regards, Anand. Anand Kumar MBBS, PhD IFOMIS Faculty of Medicine University of Leipzig H?rtelstra?e 16-18 04107 Leipzig Germany http://www.uni-leipzig.de/~akumar/ From dmb at mrc-dunn.cam.ac.uk Sat May 15 07:57:52 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat, 15 May 2004 12:57:52 +0100 (BST) Subject: [BiO BB] GeneBank to SwissProt Mapping? In-Reply-To: <2094134.1084620492070.SLOX.WebMail.wwwrun@hogwarts.imise.uni-leipzig.de> Message-ID: On Sat, 15 May 2004, Anand Kumar wrote: >Dan, > >> >> To clarify what I am doing: >> >> I take BIND protein interaction data, and for each sequence available in >> bind (with a GI accession number) I blast against SPTrEMBL. This data will >> give me a GI <-> SP accession number mapping for the dataset I am >> interested in. >> >> It will also create (as a side effect) a whole load of data about close >> homologues of the protein sequences available in BIND, which could be very >> useful. >> >> It will be easy to make a human subset of the data, for example >> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15117749&dopt=Abstract > > >Thanks for your prompt reply. Yes it would be very useful to have this >data. Since we already have the Uniprot id of human proteins, in which >we are interested (and of course their names), it would be nice to know >about their interactions with other human proteins. We have a set of >ontologies which goes from the disease level to the cellular and >subcellular level and this data will fit well with the lower level of >granularity. Our end goal is to find the collaborations by which we >wouldbe able to make a full-fledged carcinoma server, where various >carcinoma related information can be searched from the name of disease, >organ, drug, symptom, protein, cell, gene etc. Cool! You should also see the following links... http://www.rfcgr.mrc.ac.uk/GenomeWeb/prot-interaction.html including experimental protein interaction datasets and predictions. Best of luck, Dan. > >Kind Regards, >Anand. > >Anand Kumar MBBS, PhD >IFOMIS >Faculty of Medicine >University of Leipzig >H??rtelstra??e 16-18 >04107 Leipzig >Germany >http://www.uni-leipzig.de/~akumar/ > > > > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From basu at pharm.sunysb.edu Sat May 15 20:55:27 2004 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Sat, 15 May 2004 20:55:27 -0400 Subject: [BiO BB] GeneBank to SwissProt Mapping? In-Reply-To: References: Message-ID: <40A6BBFF.4010204@pharm.sunysb.edu> Hi, I used to use the xref file from here to get a mapping between swissprot,refseq and locuslink ids. ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN Check out the file human.xrefs.gz. It also do have the files for mouse and rat if go back one directory level. Hope this help. -siddhartha Dan Bolser wrote: > Thanks Pamela for your suggestions, I have tried LocusLink (the 'loc2acc' > file) but I find many missing swissprot / trembl accession numbers. I > fear that the GO mapping could be incomplete for other resons too. > > Thanks Svensson for the offer of assistance below, but I am not sure how > having PID will help me. (sorry for my ignorance). > > I know sptrembl has a good PIR mapping, can we get to PIR from GI? > > I am running blast jobs at the minuite as the bind sequence file isn't too > big, but getting accurate 1-1 mapping means that I have to blast against > the full datasets and not some non redundant version thereof. > > 4 more days to go... > > If anyone wants the data let me know. > > Dan. > From dmb at mrc-dunn.cam.ac.uk Sun May 16 13:38:01 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sun, 16 May 2004 18:38:01 +0100 (BST) Subject: [BiO BB] dumb question... Message-ID: Using the XML::Parser perl module, how can I deal with multiple XML documents concatenated into a single file? I get the following message after the first document... junk after document element at line 14075, column 0, byte 674176 at /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/XML/Parser.pm line 185 Where line 14075 is the start of the next XML document... 14075: Cheers, Dan. From anand.kumar at ifomis.uni-leipzig.de Sun May 16 13:41:55 2004 From: anand.kumar at ifomis.uni-leipzig.de (Anand Kumar) Date: Sun, 16 May 2004 19:41:55 +0200 (CEST) Subject: [BiO BB] dumb question... References: Message-ID: <1531921.1084729315786.SLOX.WebMail.wwwrun@hogwarts.imise.uni-leipzig.de> Dan, The problem is that the line 14075 is being sent to the XML parser module's handler. You could try to create a character handler before you call the parser. Once you have declared lets say $trial, you can then make a loop if $trial is equal to then read the current line and call the parser. This way your hanlder will be active BEFORE the XML parser's handler is activated and the XML parser's handler will be activated everything your handler encounters the first line of the XML file. Hope it helps. Kind Regards, Anand. Am So 16.05.2004 19:38, Dan Bolser schrieb: > > Using the XML::Parser perl module, how can I deal with multiple XML > documents concatenated into a single file? > > I get the following message after the first document... > > junk after document element at line 14075, column 0, byte 674176 at > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/XML/Parser.pm > line 185 > > Where line 14075 is the start of the next XML document... > > 14075: > > > Cheers, > Dan. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Anand Kumar MBBS, PhD IFOMIS Faculty of Medicine University of Leipzig H?rtelstra?e 16-18 04107 Leipzig Germany http://www.uni-leipzig.de/~akumar/ From roy at colibase.bham.ac.uk Mon May 17 12:26:05 2004 From: roy at colibase.bham.ac.uk (Roy Chaudhuri) Date: Mon, 17 May 2004 17:26:05 +0100 Subject: [BiO BB] Re: characterization of an incomplete genome Message-ID: <40A8E79D.4040804@colibase.bham.ac.uk> > We have assembled a Yesinia pestis genome. However, the genome is > only 95% complete. We would like to to characterize rearrangements, > large, medium size indels, repeat differences, gene differences by > comparing it with a known complete genome. > > I would appreciate if anybody could give me any advice or comments. It is possible to compare unfinished genomes with related completed genomes using BLAST and ACT (http://www.sanger.ac.uk/Software/ACT/), by concatenating the contigs into a single sequence (see: http://www.mail-archive.com/artemis-users at sanger.ac.uk/msg00107.html for a fuller description.) Roy. -- Dr. Roy Chaudhuri Bioinformatics Research Fellow, Division of Immunity and Infection, University of Birmingham, UK http://colibase.bham.ac.uk From dmb at mrc-dunn.cam.ac.uk Tue May 18 09:38:45 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Tue, 18 May 2004 14:38:45 +0100 (BST) Subject: [BiO BB] GeneBank to SwissProt Mapping? In-Reply-To: <2094134.1084620492070.SLOX.WebMail.wwwrun@hogwarts.imise.uni-leipzig.de> Message-ID: Blast derived mapping data is temporarily availible from http://interaction.mrc-dunn.cam.ac.uk/FTP/ Specifically http://interaction.mrc-dunn.cam.ac.uk/FTP/results.tab.gz The format of which is A B C D A B C D A B C D ... A = BIND GI B = SWISS ID or TREMBL ACCN C = Percent of sequence A which is identical to sequence B D = Percent of sequence B which is identical to sequence A A and B are sequence identifiers. Both C and D are required to check if one sequence is a 'subsequence' of another. e.g. A B C D 999601 G3P_THEMA 1 1 974697 Q59929 1 1 494170 Q7M0G1 1 0.4901 576205 PAR1_PAPHA 1 0.0541 196805 KAC_MOUSE 0.4472 1 896256 Q8RNV1 0.2713 1 On Sat, 15 May 2004, Anand Kumar wrote: >Dan, > >> >> To clarify what I am doing: >> >> I take BIND protein interaction data, and for each sequence available in >> bind (with a GI accession number) I blast against SPTrEMBL. This data will >> give me a GI <-> SP accession number mapping for the dataset I am >> interested in. >> >> It will also create (as a side effect) a whole load of data about close >> homologues of the protein sequences available in BIND, which could be very >> useful. >> >> It will be easy to make a human subset of the data, for example >> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15117749&dopt=Abstract > > >Thanks for your prompt reply. Yes it would be very useful to have this >data. Since we already have the Uniprot id of human proteins, in which >we are interested (and of course their names), it would be nice to know >about their interactions with other human proteins. We have a set of >ontologies which goes from the disease level to the cellular and >subcellular level and this data will fit well with the lower level of >granularity. Our end goal is to find the collaborations by which we >wouldbe able to make a full-fledged carcinoma server, where various >carcinoma related information can be searched from the name of disease, >organ, drug, symptom, protein, cell, gene etc. > >Kind Regards, >Anand. > >Anand Kumar MBBS, PhD >IFOMIS >Faculty of Medicine >University of Leipzig >H??rtelstra??e 16-18 >04107 Leipzig >Germany >http://www.uni-leipzig.de/~akumar/ > > > > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From jhao at tgen.org Tue May 18 17:36:38 2004 From: jhao at tgen.org (Jicheng Hao) Date: Tue, 18 May 2004 14:36:38 -0700 Subject: [BiO BB] Synonymous SNP finding Message-ID: <8C5AFD8EFC7B1A4EA246BA5BB1BAAE4F108D15@TGEN-M1.ad.tgen.org> I have used MUMmer to find SNPs between an incomplete genome and its reference completed genome. I then use Artemis manually to find synonymous SNPs by studying genes on the reference genome. I wonder if there is an automatic way(tool) to conduct Synonymous SNP finding. Otherwise, I have to write a tool to do that. Thank you. Jicheng Hao, Ph.D. Staff Scientist, Bioinformatics Comparative Genomics Unit Pathogen Genomics Division Translational Genomics Research Institute (TGen) 602 343 8705 (phone) 480 570 5969 (mobile) 602 343 8740 (fax) jhao at tgen.org From moyc at mail.med.upenn.edu Wed May 19 13:13:36 2004 From: moyc at mail.med.upenn.edu (Chris Moy) Date: Wed, 19 May 2004 13:13:36 -0400 Subject: [BiO BB] Re:Synonomous SNP finding In-Reply-To: <20040519160110.39F65D1F22@www.bioinformatics.org> References: <20040519160110.39F65D1F22@www.bioinformatics.org> Message-ID: > Jicheng, > You can use sequence analysis packages to do the same thing. There are > those of the commercial variety like Sequencher. That will allow you > to load a reference sequence and compare a set of other sequences > (sequenced or otherwise) and identify variability in the sequence. > This will allow you to view the electropherogram as well (if > sequencing). There is public software such as Consed available at the > Univ. of Washington that can run on unix platforms. You need do not > necessarily need to be working with sequencing data to use these > tools. Chris > On May 19, 2004, at 12:01 PM, bio_bulletin_board-request 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. Synonymous SNP finding (Jicheng Hao) > > --__--__-- > > Message: 1 > Date: Tue, 18 May 2004 14:36:38 -0700 > From: "Jicheng Hao" > To: > Subject: [BiO BB] Synonymous SNP finding > Reply-To: bio_bulletin_board at bioinformatics.org > > I have used MUMmer to find SNPs between an incomplete genome and its > reference completed genome. I then use Artemis manually to find > synonymous SNPs by studying genes on the reference genome. > > I wonder if there is an automatic way(tool) to conduct Synonymous SNP > finding. Otherwise, I have to write a tool to do that. > > Thank you. > > Jicheng Hao, Ph.D. > Staff Scientist, Bioinformatics > Comparative Genomics Unit > Pathogen Genomics Division=20 > Translational Genomics Research Institute (TGen)=20 > 602 343 8705 (phone) > 480 570 5969 (mobile) > 602 343 8740 (fax) > jhao at tgen.org > > > --__--__-- > > _______________________________________________ > 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 landman at scalableinformatics.com Fri May 21 09:34:53 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Fri, 21 May 2004 09:34:53 -0400 Subject: [BiO BB] updated x86_64 mpiBLAST rpms available Message-ID: <1085146492.2551.18.camel@protein.scalableinformatics.com> Hi folks: I updated the mpiBLAST (http://mpiblast.lanl.gov) RPMs that we are hosting off of http://scalableinformatics.com . The 1.2.1-1 source RPM would not build cleanly on an x86_64 platform. This has been fixed, and we built binaries for SUSE 9.0 AMD. If there is interest, we may build some for Fedora Core 2, and other platforms, though the source RPM is there for you as well. See http://downloads.scalableinformatics.com/downloads/mpiblast/ for the updated packages (1.2.1-2). Older packages will be archived by next week. Joe -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From bb2duprm at uco.es Fri May 21 11:49:10 2004 From: bb2duprm at uco.es (bb2duprm at uco.es) Date: Fri, 21 May 2004 17:49:10 +0200 (MET DST) Subject: [BiO BB] molecular modelling In-Reply-To: <20040520160106.A5276D1F24@www.bioinformatics.org> References: <20040520160106.A5276D1F24@www.bioinformatics.org> Message-ID: <1085154550.40ae24f61fe03@www.uco.es> I have a question about molecular modelling. I have the 3D structure of a protein and I would like to know the effect that one mutation produces into that structure. I only have free tools, like Swiss PDB Viwer, Modeller, etc. Someone knows how can I do it or what software could I use to that purpose? Thank you very much. Mario From dmb at mrc-dunn.cam.ac.uk Fri May 21 12:37:19 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 21 May 2004 17:37:19 +0100 (BST) Subject: [BiO BB] molecular modelling In-Reply-To: <1085154550.40ae24f61fe03@www.uco.es> Message-ID: On Fri, 21 May 2004 bb2duprm at uco.es wrote: >I have a question about molecular modelling. I have the 3D structure of >a protein and I would like to know the effect that one mutation produces >into that structure. I only have free tools, like Swiss PDB Viwer, >Modeller, etc. Someone knows how can I do it or what software could I >use to that purpose? Thank you very much. You could try YASARA, but chances are you would never see a major change in structure after changing 1 AA (although the AA may be critical for folding in vivo). You could try measuring the energy of the structure before and after the change (with some minimization) to see if the resulting structure is 'unstable'. If you are looking at a very specific thing, like a binding site residue, YASARA should do the job perfectly. > >Mario >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From szed4 at yahoo.com Fri May 21 14:38:05 2004 From: szed4 at yahoo.com (Shamshad Zarina) Date: Fri, 21 May 2004 11:38:05 -0700 (PDT) Subject: [BiO BB] molecular modelling In-Reply-To: <1085154550.40ae24f61fe03@www.uco.es> Message-ID: <20040521183805.96620.qmail@web14008.mail.yahoo.com> Hi Mario, I think you can use online server of Whatif for creating a mutation in your protein. Best, Shamshad --- bb2duprm at uco.es wrote: > I have a question about molecular modelling. I have > the 3D structure of a protein and I > would like to know the effect that one mutation > produces into that structure. I only have > free tools, like Swiss PDB Viwer, Modeller, etc. > Someone knows how can I do it or what > software could I use to that purpose? > Thank you very much. > > Mario > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________ Do you Yahoo!? Yahoo! Domains ? Claim yours for only $14.70/year http://smallbusiness.promotions.yahoo.com/offer From landman at scalableinformatics.com Mon May 24 10:49:06 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Mon, 24 May 2004 10:49:06 -0400 Subject: [BiO BB] NCBI-2.2.9 rpms available Message-ID: <1085410145.5412.98.camel@protein.scalableinformatics.com> Folks: RPM's (including the source RPM) of NCBI Toolkit 2.2.9 are available from http://downloads.scalableinformatics.com/downloads/ncbi . These RPMs are for i686 (pentium 4 and higher), athlon, x86_64, and source. They include our Opteron patch to compile the x86_64 binaries. The athlon and x86_64 RPMs were built on SuSE 9.0, and the i686 was built on RHEL 3.0. Please report any bugs to us. Joe -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From senthil at www.cdfd.org.in Tue May 25 00:26:14 2004 From: senthil at www.cdfd.org.in (Mr M senthil kumar) Date: Tue, 25 May 2004 10:56:14 +0630 Subject: [BiO BB] R for Bioinformatics Message-ID: Hi, Does anyone know about this title (R for Bioinformatics) from O'Reilly. I have searched the publisher's site and I have googled too, but i am unable to find anything. I need to know the table of contents, when it will be available and mainly what it is all about! Thanks in advance. Senthil From idoerg at burnham.org Tue May 25 12:19:26 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 25 May 2004 09:19:26 -0700 Subject: [BiO BB] Re: R for Bioinformatics In-Reply-To: <20040525160108.DE763D1F15@www.bioinformatics.org> References: <20040525160108.DE763D1F15@www.bioinformatics.org> Message-ID: <40B3720E.4000905@burnham.org> Says here: http://www.rbookshop.com/science/b/Bioinformatics/R_for_Bioinformatics_059600544X.htm That it's slotted for November, 2004. No TOC or synposis. As a lightweight R user, I definitely prepare to have a looksee once it is out. Iddo bio_bulletin_board-request 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. R for Bioinformatics (Mr M senthil kumar) > > --__--__-- > > Message: 1 > Date: Tue, 25 May 2004 10:56:14 +0630 > From: Mr M senthil kumar > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] R for Bioinformatics > Reply-To: bio_bulletin_board at bioinformatics.org > > Hi, > > Does anyone know about this title (R for Bioinformatics) from O'Reilly. I > have searched the publisher's site and I have googled too, but i am unable > to find anything. I need to know the table of contents, when it will be > available and mainly what it is all about! > > Thanks in advance. > > Senthil > > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest > > -- 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 hjm at tacgi.com Tue May 25 11:45:00 2004 From: hjm at tacgi.com (Harry Mangalam) Date: Tue, 25 May 2004 08:45:00 -0700 Subject: [BiO BB] R for Bioinformatics In-Reply-To: References: Message-ID: <40B369FC.7080609@tacgi.com> I suspect it is a book about the Bioconductor project, which is reasonably well documented at the web site: http://www.bioconductor.org/ bioC is mostly for gene expression analysis at this point, but it is moving into other areas in bioinformatics in which statistics can be applied to good effect. BioC is writ in R so some familiarity with R is required: http://r-project.org hjm Mr M senthil kumar wrote: > Hi, > > Does anyone know about this title (R for Bioinformatics) from O'Reilly. I > have searched the publisher's site and I have googled too, but i am unable > to find anything. I need to know the table of contents, when it will be > available and mainly what it is all about! > > Thanks in advance. > > Senthil > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Cheers, Harry Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com <> From TAN_Tsu_Soo at nyp.gov.sg Tue May 25 20:43:39 2004 From: TAN_Tsu_Soo at nyp.gov.sg (TAN_Tsu_Soo at nyp.gov.sg) Date: Wed, 26 May 2004 08:43:39 +0800 Subject: [BiO BB] R for Bioinformatics Message-ID: You can do search at Amazon.com. some information is available there, including price! Release date is November 2004. TS Tan Date: Tue, 25 May 2004 10:56:14 +0630 From: Mr M senthil kumar To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] R for Bioinformatics Reply-To: bio_bulletin_board at bioinformatics.org Hi, Does anyone know about this title (R for Bioinformatics) from O'Reilly. I have searched the publisher's site and I have googled too, but i am unable to find anything. I need to know the table of contents, when it will be available and mainly what it is all about! Thanks in advance. Senthil From risea at cecalc.ula.ve Thu May 27 12:06:15 2004 From: risea at cecalc.ula.ve (Raul Isea) Date: Thu, 27 May 2004 12:06:15 -0400 (VET) Subject: [BiO BB] Curso =?iso-8859-1?Q?B=E1sico_en_Epidemiolog=EDa_Molecular_?= (Becas DISPONIBLES) Message-ID: <4511.150.185.138.94.1085673975.squirrel@fubar.ula.ve> La Red Latinoamericana en Epidemiolog?a Molecular perteneciente al Programa de Biotecnologia para Am?rica Latina y el Caribe de la Universidad de las Naciones Unidas (UNU-BIOLAC), el Instituto Venezolano de Investigaciones Cient?ficas y el Centro Nacional de C?lculo Cient?fico Universidad de Los Andes (CeCalCULA) tienen el agrado de anunciar el curso: "Curso B?sico en Epidemiolog?a Molecular" http://www.saber.ula.ve/eventos/epidemiologia_molecular/ que se va a realizar en la Universidad de Los Andes - M?rida (Venezuela) del 12 al 17 de julio de 2004 en el Auditorio de Ingenier?a. El objetivo del curso es proveer al estudiante con las herramientas b?sicas para interpretar datos moleculares en el contexto de investigaciones epidemiol?gicas. BECAS: Hay Becas disponibles para estadia en Merida y para cancelar el pasaje aereo previa solicitud de las personas interesadas! PROGRAMA DEL CURSO: * Conceptos B?sicos en Epidemiolog?a: usando marcadores moleculares (por la Dra. Lyda Osorio - Colombia) * Panorama sobre las t?cnicas para el estudio de variaci?n gen?tica (por el Dr. Ludmel Urdaneta - Venezuela) * Conceptos b?sicos en gen?tica de poblaciones (por el Dr. Ananias Escalante - Venezuela) * Recombinaci?n y "Linkage Disequilibrium" (por el Dr. Marcelo Ferreira - Brasil) * Estructuras de Poblaciones (por la Dra. Valeria Souza - M?xico) * Una revisi?n sobre m?todos de sistem?tica molecular (por el Dr. Marcelo Briones - Brasil) * Epidemiolog?a molecular y entomolog?a medica (por el Dr. Fernando Monteiro - Brasil) Requisitos: *Los participantes deben ser capaces de entender clases y leer material en el idioma ingles. *Todos los participantes deben tener un curso b?sico de estad?stica y probabilidad. *Los participantes deben demostrar legitimo inter?s en realizar investigaciones epidemiol?gicas. *Conocimiento de t?cnicas de laboratorio utilizadas en epidemiolog?a molecular (PCR, RFLP, RAPDs, Secuenciaci?n) *En caso de ser Estudiante de postgrado, agregar una peque?a justificaci?n del por qu? desea tomar este curso. Se van a incluir sesiones de computaci?n para ense?ar al estudiante el uso de programas de computaci?n de dominio p?blico (Previa selecci?n de los mismos y con un cupo m?ximo de hasta 25 personas). PATROCINANTES: *UNU/Biolac (United Nations University / Biotechnology for Latin America and The Caribbean). *Latin American Network in Molecular Epidemiology (LANMEp) *Centers for Disease Control and Prevention. *Instituto Venezolano de Investigaciones Cient?ficas. *Universidad de Los Andes (ULA). *Centro Nacional de C?lculo Cient?fico (CeCalCULA). *Organizaci?n Panamericana de la Salud (OPS). Inscripciones: Para hacer su inscripci?n, envi? dos referencias as? como la planilla de inscripci?n que se anexa en este correo electr?nico a bioinfo at cecalc.ula.ve. Mayor Informaci?n: Centro Nacional de Calculo Cient?fico Universidad de los Andes, CeCalCULA. Centro Profesional Masini, Av.4 entre calles 18 y 19, Piso 3, Ofic. B-32, M?rida 5101, Venezuela Telf. +58-274-2524192 fax: +58-274-2525473 E-mail: bioinfo at cecalc.ula.ve Detalles en http://www.saber.ula.ve/eventos/epidemiologia_molecular/ Por el Comit? Organizador Raul Isea -- **** Dr. Raul Isea PhD in Chemistry Email: risea at cecalc.ula.ve http://www.cecalc.ula.ve/~risea (Mirror at http://www.geocities.com/lrisea) Fax in USA : 1(208)978-2122 Fax in Venezuela: 58 (274) 2525473 -------------- next part -------------- A non-text attachment was scrubbed... Name: registration-taller.rtf Type: text/richtext Size: 17319 bytes Desc: not available URL: From lon at lonjames.com Tue May 25 12:55:41 2004 From: lon at lonjames.com (L. S. James) Date: Wed, 26 May 2004 01:55:41 +0900 (JST) Subject: [BiO BB] Re: joe conway, statistical tools 'R' In-Reply-To: <20040525160108.DE763D1F15@www.bioinformatics.org> References: <20040525160108.DE763D1F15@www.bioinformatics.org> Message-ID: <48130.216.27.177.107.1085504141.squirrel@216.27.177.107> An HTML attachment was scrubbed... URL: From rossini at blindglobe.net Tue May 25 13:11:59 2004 From: rossini at blindglobe.net (A.J. Rossini) Date: Tue, 25 May 2004 10:11:59 -0700 Subject: [BiO BB] R for Bioinformatics In-Reply-To: <40B369FC.7080609@tacgi.com> (Harry Mangalam's message of "Tue, 25 May 2004 08:45:00 -0700") References: <40B369FC.7080609@tacgi.com> Message-ID: <854qq44ejk.fsf@servant.blindglobe.net> It covers that a bit, but supposedly it's a bit more general than just gene expression array analysis. I saw an early description a while back when it was being proposed (1-2 years back?), but not recently. best, -tony Harry Mangalam writes: > I suspect it is a book about the Bioconductor project, which is > reasonably well documented at the web site: > > http://www.bioconductor.org/ > > bioC is mostly for gene expression analysis at this point, but it is > moving into other areas in bioinformatics in which statistics can be > applied to good effect. > > BioC is writ in R so some familiarity with R is required: > > http://r-project.org > > hjm > > > Mr M senthil kumar wrote: >> Hi, >> Does anyone know about this title (R for Bioinformatics) from >> O'Reilly. I >> have searched the publisher's site and I have googled too, but i am unable >> to find anything. I need to know the table of contents, when it will be >> available and mainly what it is all about! >> Thanks in advance. >> Senthil >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > > -- > Cheers, Harry > Harry J Mangalam - 949 856 2847 (v&f) - hjm at tacgi.com > <> > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- rossini at u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachments may be confidential and privileged. If you received this message in error, please destroy it and notify the sender. Thank you. From dmb at mrc-dunn.cam.ac.uk Sat May 29 09:22:27 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat, 29 May 2004 14:22:27 +0100 (BST) Subject: [BiO BB] download uniparc? Message-ID: Why is their no unipark ftp site? Is their any any way to get a dump of all the xrefs from uniparc? Why are the uniparc xrefs not part of uniprot? Any body know?