From idoerg at burnham.org Wed Jul 5 17:00:14 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 05 Jul 2006 14:00:14 -0700 Subject: [BiO BB] AFP early registration cutoff: only 10 days left! Message-ID: <44AC285E.2090403@burnham.org> (Please forward as appropriate) Only 10 days left for early registration to the Second Automated Function Prediction Meeting. Do not miss the opportunity to attend this meeting on an pivotal emerging topic in bioinformatics. Early registration ends July 15, 2006. Sequence and structure genomics have generated a wealth of data, but extracting meaningful information from genomic information is becoming an increasingly difficult challenge. Both the number and the diversity of discovered genes is increasing. This increase means that established annotation methods, such as homology transfer, are annotating less data. In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software which is out there. We probably know the sequence of the target for next generation antibiotics or cancer treatment. We just do not realize that because the target is currently annotated as a "domain of unknown function". For these reasons and many more, automated protein function prediction is rapidly gaining interest among computational biologists in academia and industry. The second AFP meeting will be a three day event, August 30-September 1, 2006 on the campus of University of California, San Diego,California, USA. AFP 2006 will feature: * Eight keynote talks delivered by leading researchers in the field * Nineteen Submitted talks * Conference proceedings published as research papers in BMC Bioinformatics * A special discussion panel on gene and protein annotation * A poster session Keynote speakers: * Russ B. Altman, Stanford University, USA * Philip E. Bourne, University of California, San Diego, USA * Steven E. Brenner, University of California, Berkeley, USA * Terry Gaasterland, Scripps Institute of Oceanography, La Jolla, USA * Adam Godzik, Burnham Institute for Medical Research and University of California, San Diego USA * Christos Ouzounis European Bioinformatics Institute, Cambridge, UK * Anna Tramontano, University of Rome, "La Sapienza", Rome, Italy * Shoshana Wodak, Hospital for Sick Children, and Departments of Biochemistry and Medical Genetics, University of Toronto, Canada. Register now: http://BioFunctionPrediction.org/AFP/afp06/registration/ Program, including extended talk abstracts: http://BioFunctionPrediction.org/AFP/afp06/program/ Travel: http://BioFunctionPrediction.org/AFP/afp06/travel/ For more information please see the meeting site: http://BioFunctionPrediction.org/AFP/afp06 Sincerely, Iddo Friedberg, in the name of the AFP 2006 organizing committee -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9949 http://iddo-friedberg.org http://BioFunctionPrediction.org From christoph.gille at charite.de Thu Jul 6 15:00:33 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Thu, 6 Jul 2006 21:00:33 +0200 (CEST) Subject: [BiO BB] Macintosh help needed Message-ID: <62290.84.190.45.99.1152212433.squirrel@webmail.charite.de> I am developing a free program for protein analysis using an IBM PC. Today I had the opportunity to test it on MacOSX and encountered some problems. I am now going to change a few things to get it running on Mac. Has anybody got a minute to quickly check the fixed version on a Mac? Many thanks Christoph From jeremymann at gmail.com Thu Jul 6 15:40:59 2006 From: jeremymann at gmail.com (Jeremy Mann) Date: Thu, 6 Jul 2006 14:40:59 -0500 Subject: [BiO BB] Macintosh help needed In-Reply-To: <62290.84.190.45.99.1152212433.squirrel@webmail.charite.de> References: <62290.84.190.45.99.1152212433.squirrel@webmail.charite.de> Message-ID: <79ec289f0607061240h24c7ef45ia2e22df3f89860e7@mail.gmail.com> Do you need an Intel or PPC Mac? On 7/6/06, Dr. Christoph Gille wrote: > I am developing a free program for protein analysis using an IBM PC. > Today I had the opportunity to test it on MacOSX and encountered some problems. > I am now going to change a few things to get it running on Mac. > Has anybody got a minute to quickly check the fixed version on a Mac? > Many thanks > Christoph > > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Jeremy From austin.tanney at almacgroup.com Fri Jul 7 03:44:01 2006 From: austin.tanney at almacgroup.com (Tanney, Austin) Date: Fri, 7 Jul 2006 08:44:01 +0100 Subject: [BiO BB] Macintosh help needed Message-ID: I can do it on a PPC if you want to send it to me... Austin -----Original Message----- From: bio_bulletin_board-bounces+austin.tanney=almac-diagnostics.com at bioinform atics.org [mailto:bio_bulletin_board-bounces+austin.tanney=almac-diagnostics.com at b ioinformatics.org]On Behalf Of Dr. Christoph Gille Sent: 06 July 2006 20:01 To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Macintosh help needed I am developing a free program for protein analysis using an IBM PC. Today I had the opportunity to test it on MacOSX and encountered some problems. I am now going to change a few things to get it running on Mac. Has anybody got a minute to quickly check the fixed version on a Mac? Many thanks Christoph _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Proprietary or confidential information belonging to Almac Group Limited or to one of its affiliated companies may be contained in this message. 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From christoph.gille at charite.de Fri Jul 7 10:52:09 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Fri, 7 Jul 2006 16:52:09 +0200 (CEST) Subject: [BiO BB] Macintosh help needed In-Reply-To: References: Message-ID: <38465.141.42.56.114.1152283929.squirrel@webmail.charite.de> Dear Austin, thanks for this nice offer It is found at http://3d-alignment.eu/ and requires OSX The main problem is already fixed. I expect many more tiny problems. Does the introduction tutorial work ? Have a nice week-end Christoph From codeshepherd at gmail.com Fri Jul 7 14:37:16 2006 From: codeshepherd at gmail.com (Deepan Chakravarthy) Date: Sat, 08 Jul 2006 00:07:16 +0530 Subject: [BiO BB] spell checker for biological words Message-ID: <1152297436.15725.2.camel@localhost.localdomain> Hello, I am hunting for a opensource biological spell checker. If someone is familiar with an algorithm for writing one.. then please do comment on the same. thanks Deepan Home Page: www.codeshepherd.com Fun Page: www.sudoku-solver.net/sudoku.html From colman at uci.edu Sat Jul 8 11:39:39 2006 From: colman at uci.edu (Richard Colman) Date: Sat, 8 Jul 2006 08:39:39 -0700 Subject: [BiO BB] What do you use for MSA and Design? Message-ID: <006301c6a2a4$ba03b820$6e456f44@D8N17S91> I am currently working on a computer user interface for specifying (not designing) mutational protein libraries. In addition to a "online forms interface" I would like to be able to directly import protein sequence data and multiple sequence alignments from a file. I was wondering whether any researchers would like to comment on what types of programs and data formats are popular. In paticular, I am considering an function to directly import Excel spreadsheet files (ala GoCore, etc.), FASTA with alignments preserved, or ???? Any comments would be greatly appreciated. Rick Colman UC Irvine From felipe.albrecht at gmail.com Sat Jul 8 14:12:55 2006 From: felipe.albrecht at gmail.com (Felipe Albrecht) Date: Sat, 8 Jul 2006 15:12:55 -0300 Subject: [BiO BB] Least Square Methods Message-ID: Hi, Im searching techniques for inferring phylogenies and I see the "Least Square methods". I read that have some algorithms that implements this methods with considerable differences. So, I search in Joe Felsenstein's book about this algorithms, but I only found "how it works" and not some algorithms descriptions. I also read the Fitch and Kitsch programs source, but I continue with many doubts regarding the least square algorithms. Some one haves a algorithm in computational or mathematics format ? Or a simple computer implementation? Thanks Felipe Albrecht From hershel.safer at weizmann.ac.il Sun Jul 9 03:10:10 2006 From: hershel.safer at weizmann.ac.il (Hershel Safer) Date: Sun, 09 Jul 2006 10:10:10 +0300 Subject: [BiO BB] ECCB workshops: Call for papers & posters Message-ID: <44B0ABD2.9040101@weizmann.ac.il> ECCB workshops: Call for papers and posters 5th European Conference on Computational Biology - ECCB '06 September 10-13, 2006 Eilat, Israel www.eccb06.org Papers and posters are solicited for two full-day workshops that will be held on the first day of ECCB, Sunday, September 10. ** BioSapiens Workshop on Genome Annotation http://www.eccb06.org/new_pages/program/program_workshops.html#ws2 This workshop, sponsored by the BioSapiens consortium, will bring together an international group of experts to discuss functional aspects of genome annotation. The goals are to create an open forum to discuss current problems on function annotation, to foster the analysis of key scientific issues in function prediction, and promote collaboration among scientists interested in the development of computational methods in this key area of molecular biology and to foster the interactions between computational and experimental scientists in the field. The program will cover five topics: 1. Large scale studies of membrane proteins 2. Whole genomes annotation 3. Alternative splicing 4. Structural genomics 5. Cross-indexing between biological databases Posters will be accepted on a first-come, first-served basis, until August 10. ** Distributed, High-Performance & Grid Computing in Computational Biology (GCCB) http://www.eccb06.org/new_pages/program/program_workshops.html#ws1 http://gccb2006.ulster.ac.uk/-Introduction-.html The GCCB Workshop will bring together computational biologists, bioinformaticians, and life scientists who have researched and applied distributed, high-performance and grid computing technologies in the context of computational biology and bioinformatics. The workshop will discuss innovative work in progress and important new directions. Contributions of interest will address topics related to the development, deployment, application and evaluation of distributed, high-performance and grid computing technologies in the context of the following computational biology and bioinformatics areas. The deadline for submitting manuscripts is July 15. Accepted papers will be presented orally or as posters at the workshop. Selected accepted papers will be published in Springer's LNBI proceedings. From mmarchywka at eyewonder.com Sun Jul 9 09:44:48 2006 From: mmarchywka at eyewonder.com (Mike Marchywka) Date: Sun, 9 Jul 2006 09:44:48 -0400 Subject: [BiO BB] spell checker for biological words Message-ID: <73CA026E5E77C74398C69F3338C5967C07553E58@atlexc01.atlanta.eyewonder.com> On a related topic, does anyone know where to get good lists of chemical names ( systematic and trivial )? I hunted around iupac site for a while and could extract some for organic things but I really had to play with it and it isn't quite complete. The FDA has some drug listings that are fairly easy to parse with bash to extract drug vocabularies. While I don't need a spell checker, this does come up when you want to scan patents or SEC filings for word catagories. There is probably something obvious on google related to this but I haven't found it. Word catagorization is probably a common interest in many text analysis issues. If you are really looking for spell check algorithms, sometimes citeseer has some nice articles. This seems to have come up on cpan before: http://search.cpan.org/dist/Text-Aspell/Aspell.pm http://www.cpanforum.com/posts/2165 You could probably write a simple one in a few lines of PERL but I don't know offhand where to get a dictionary. Their hashs do a lot of thrashing when they get too big and I've never figured out how to fix this ( and I don't hold out a lot of hope with cygwin either :)). -----Original Message----- From: bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformati cs.org]On Behalf Of Deepan Chakravarthy Sent: FridayJuly-07-2006 02:37 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] spell checker for biological words Hello, I am hunting for a opensource biological spell checker. If someone is familiar with an algorithm for writing one.. then please do comment on the same. thanks Deepan Home Page: www.codeshepherd.com Fun Page: www.sudoku-solver.net/sudoku.html _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Sun Jul 9 11:05:11 2006 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sun, 09 Jul 2006 16:05:11 +0100 Subject: [BiO BB] spell checker for biological words In-Reply-To: <73CA026E5E77C74398C69F3338C5967C07553E58@atlexc01.atlanta.eyewonder.com> References: <73CA026E5E77C74398C69F3338C5967C07553E58@atlexc01.atlanta.eyewonder.com> Message-ID: <44B11B27.5010206@mrc-dunn.cam.ac.uk> Mike Marchywka wrote: > On a related topic, does anyone know where to get good lists > of chemical names ( systematic and trivial )? > I hunted around iupac site for a while and could extract > some for organic things but I really had to play with > it and it isn't quite complete. > > The FDA has some drug listings that are fairly easy to parse with > bash to extract drug vocabularies. > > While I don't need a spell checker, this does come up when > you want to scan patents or SEC filings for word catagories. > There is probably something obvious on google > related to this but I haven't found it. Word catagorization > is probably a common interest in many text analysis issues. > > If you are really looking for spell check algorithms, > sometimes citeseer has some nice articles. > You can grab lists of systematic protein and chemical names from KEGG (who provide nice versions of ENZYME and LIGAND databases). I zapped the systematic protein names through aspell, which makes things a lot easier. > > This seems to have come up on cpan before: > http://search.cpan.org/dist/Text-Aspell/Aspell.pm > http://www.cpanforum.com/posts/2165 > > You could probably write a simple one in a few lines of PERL but > I don't know offhand where to get a dictionary. > Their hashs do a lot of thrashing when they get too big > and I've never figured out how to fix this ( and I don't > hold out a lot of hope with cygwin either :)). > > > > > -----Original Message----- > From: > bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.org > [mailto:bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformati > cs.org]On Behalf Of Deepan Chakravarthy > Sent: FridayJuly-07-2006 02:37 PM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] spell checker for biological words > > > Hello, > I am hunting for a opensource biological spell checker. If someone is > familiar with an algorithm for writing one.. then please do comment on > the same. > thanks > Deepan > Home Page: www.codeshepherd.com > Fun Page: www.sudoku-solver.net/sudoku.html > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From ishwarayasam at gmail.com Sun Jul 9 06:53:40 2006 From: ishwarayasam at gmail.com (sindhu sambandam) Date: Sun, 9 Jul 2006 03:53:40 -0700 Subject: [BiO BB] help Message-ID: hi everyone this is Ishwaraya from India..i'm an under graduate student doing my final year...i'm interested in doing my project in bioinformatics...but i dont find much resoures or guides to help me...i want to develop softwares for 2D to 3D conversion or work with drug designing..i have a paper called drug designing and molecular modelling for which i 've no faculties...i'm helpless here having that subject in the last year of study...can this organisation or anyone help me with my work and guiide and teach ...pl ishwaraya -------------- next part -------------- An HTML attachment was scrubbed... URL: From harry.mangalam at uci.edu Mon Jul 10 12:53:32 2006 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Mon, 10 Jul 2006 09:53:32 -0700 Subject: [BiO BB] What do you use for MSA and Design? In-Reply-To: <006301c6a2a4$ba03b820$6e456f44@D8N17S91> References: <006301c6a2a4$ba03b820$6e456f44@D8N17S91> Message-ID: <200607100953.33975.harry.mangalam@uci.edu> Hi Rick, You don't say what kind of data you're importing, which will drive the decision. If the info is available or if you can configure the eventual output, the clustal output format (.msa) is quite well-supported among downstream applications. If you're trying to maintain phylogenetic info, the Phylip format (.dnd) is well supported as well. If you only have html output then you're in for some parsing. I'm not familiar with GoCore output, but if it's a Excel-based format, you can extract the contents via perl's parseexcel modules altho complex links and structure will probably be lost. On the other hand, most large-scale analyses don't relay on point&click apps as a part of the analysis for obvious reasons, so unless gocore provides some kind of exceptional analysis (it doesn't appear to, via an admittedly fast drive-by of the site), it's probably more appropriate to use one of the more programmable/scriptable analysis tools available to produce the data in the 1st place. hjm On Saturday 08 July 2006 08:39, Richard Colman wrote: > I am currently working on a computer user interface for specifying > (not designing) mutational protein libraries. In addition to a > "online forms interface" I would like to be able to directly import > protein sequence data and multiple sequence alignments from a file. > > I was wondering whether any researchers would like to comment on > what types of programs and data formats are popular. In paticular, > I am considering an function to directly import Excel spreadsheet > files (ala GoCore, etc.), FASTA with alignments preserved, or ???? > > Any comments would be greatly appreciated. > > Rick Colman > UC Irvine > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Harry Mangalam - Research Computing at NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824 0084(o), 949 285 4487(c) harry.mangalam at uci.edu From uma_25984 at yahoo.co.in Tue Jul 11 11:06:21 2006 From: uma_25984 at yahoo.co.in (umaa) Date: Tue, 11 Jul 2006 16:06:21 +0100 (BST) Subject: [BiO BB] help In-Reply-To: Message-ID: <20060711150621.6424.qmail@web8713.mail.in.yahoo.com> hi ishwarya, visit www.helixinfosystems.com for ur answers sindhu sambandam wrote: hi everyone this is Ishwaraya from India..i'm an under graduate student doing my final year...i'm interested in doing my project in bioinformatics...but i dont find much resoures or guides to help me...i want to develop softwares for 2D to 3D conversion or work with drug designing..i have a paper called drug designing and molecular modelling for which i 've no faculties...i'm helpless here having that subject in the last year of study...can this organisation or anyone help me with my work and guiide and teach ...pl ishwaraya _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Uma --------------------------------- Find out what India is talking about on Yahoo! Answers India. So, what?s NEW about the NEW Yahoo! Messenger? Find out. -------------- next part -------------- An HTML attachment was scrubbed... URL: From narcis at fiserlab.org Tue Jul 11 14:19:47 2006 From: narcis at fiserlab.org (Narcis Fernandez-Fuentes) Date: Tue, 11 Jul 2006 14:19:47 -0400 Subject: [BiO BB] scop pairwise alignment In-Reply-To: <20060711150621.6424.qmail@web8713.mail.in.yahoo.com> References: <20060711150621.6424.qmail@web8713.mail.in.yahoo.com> Message-ID: <44B3EBC3.30603@fiserlab.org> Hi all, Does anybody know where to find sequence pairwise alignment derived from SCOP database? I tried PALI but they don't provide parseable files. Thanks! From jeff at bioinformatics.org Tue Jul 11 14:56:03 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 11 Jul 2006 14:56:03 -0400 Subject: [BiO BB] help In-Reply-To: References: Message-ID: <44B3F443.1060806@bioinformatics.org> By "2D to 3D conversion or work with drug designing", I assume Ishwaraya is looking for resources on modeling and structure prediction. I think joining an open-source project would be helpful. Bioinformatics.Org also has a mailing list on molecular visualization: http://bioinformatics.org/lists/molvis-list Cheers, Jeff sindhu sambandam wrote: > hi everyone > this is Ishwaraya from India..i'm an under graduate student doing my > final year...i'm interested in doing my project in bioinformatics...but > i dont find much resoures or guides to help me...i want to develop > softwares for 2D to 3D conversion or work with drug designing..i have a > paper called drug designing and molecular modelling for which i 've no > faculties...i'm helpless here having that subject in the last year of > study...can this organisation or anyone help me with my work and guiide > and teach ...pl > ishwaraya -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From dmb at mrc-dunn.cam.ac.uk Wed Jul 12 03:59:30 2006 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 12 Jul 2006 08:59:30 +0100 Subject: [BiO BB] help In-Reply-To: <44B3F443.1060806@bioinformatics.org> References: <44B3F443.1060806@bioinformatics.org> Message-ID: <44B4ABE2.9070300@mrc-dunn.cam.ac.uk> J.W. Bizzaro wrote: > By "2D to 3D conversion or work with drug designing", I assume Ishwaraya > is looking for resources on modeling and structure prediction. I think > joining an open-source project would be helpful. Bioinformatics.Org > also has a mailing list on molecular visualization: > > http://bioinformatics.org/lists/molvis-list > > Cheers, > Jeff > > sindhu sambandam wrote: > >> hi everyone >> this is Ishwaraya from India..i'm an under graduate student doing my >> final year...i'm interested in doing my project in >> bioinformatics...but i dont find much resoures or guides to help >> me...i want to develop softwares for 2D to 3D conversion or work with >> drug designing..i have a paper called drug designing and molecular >> modelling for which i 've no faculties...i'm helpless here having that >> subject in the last year of study...can this organisation or anyone >> help me with my work and guiide and teach ...pl >> ishwaraya > I have an (embarrassingly) small list of 2D -> 3D software here; http://www.bioinformatics.org/scol/links.html I will try to update that site to a Wiki, so we can all contribute to such mini 'knowledge bases'. Dan. From hamid at ibb.ut.ac.ir Thu Jul 13 08:04:42 2006 From: hamid at ibb.ut.ac.ir (hamid) Date: Thu, 13 Jul 2006 16:34:42 +0430 Subject: [BiO BB] Finding introns and exons.. In-Reply-To: <44B3F443.1060806@bioinformatics.org> References: <44B3F443.1060806@bioinformatics.org> Message-ID: Hi buddy, I need to extract all introns and exons of an organism such as D. melanogaster. How can I download all of the introns and exons as a bunch? From ishwarayasam at gmail.com Wed Jul 12 07:35:34 2006 From: ishwarayasam at gmail.com (sindhu sambandam) Date: Wed, 12 Jul 2006 04:35:34 -0700 Subject: [BiO BB] help In-Reply-To: <44B3F443.1060806@bioinformatics.org> References: <44B3F443.1060806@bioinformatics.org> Message-ID: hi jeff i'm trying to to do my 6 months project work in software development...of which i chose to do 2D to 3D conversion...i've still not decided not that because being an undergraduate student in biotechnology i dont know how far its possible...but i'm interested in working in this area regarding drug designing...its a part of my curriculum...people told me its a paper not meant for under graduates...they say its tough and difficult to understand....thats why i needed someone to guide... On 7/11/06, J.W. Bizzaro wrote: > > By "2D to 3D conversion or work with drug designing", I assume Ishwaraya > is > looking for resources on modeling and structure prediction. I think > joining an > open-source project would be helpful. Bioinformatics.Org also has a > mailing > list on molecular visualization: > > http://bioinformatics.org/lists/molvis-list > > Cheers, > Jeff > > sindhu sambandam wrote: > > hi everyone > > this is Ishwaraya from India..i'm an under graduate student doing my > > final year...i'm interested in doing my project in bioinformatics...but > > i dont find much resoures or guides to help me...i want to develop > > softwares for 2D to 3D conversion or work with drug designing..i have a > > paper called drug designing and molecular modelling for which i 've no > > faculties...i'm helpless here having that subject in the last year of > > study...can this organisation or anyone help me with my work and guiide > > and teach ...pl > > ishwaraya > > -- > J.W. Bizzaro > Bioinformatics Organization, Inc. (Bioinformatics.Org) > E-mail: jeff at bioinformatics.org > Phone: +1 508 890 8600 > -- > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From christoph.gille at charite.de Thu Jul 13 03:11:18 2006 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Thu, 13 Jul 2006 09:11:18 +0200 (CEST) Subject: [BiO BB] Finding introns and exons.. In-Reply-To: References: <44B3F443.1060806@bioinformatics.org> Message-ID: <64567.84.190.34.140.1152774678.squirrel@webmail.charite.de> > I need to extract all introns and exons of an organism such as D. > melanogaster. the ENSEMBL database can be downloaded. From schnee at ipk-gatersleben.de Thu Jul 13 08:28:15 2006 From: schnee at ipk-gatersleben.de (Roland Schnee) Date: Thu, 13 Jul 2006 14:28:15 +0200 Subject: [BiO BB] Call for Abstracts - DWTB2006 Message-ID: <007101c6a677$d0b80e00$868a5ec2@ta14> Dear all, we are organising a workshop on data warehouse issues in bioinformatics that covers warehouse techniques AND applications/tools to be used via a warehouse from 4-6 Dec, 2006 in Wittenberg, Germany. Language will be Engish. If you are interested in sending an abstract, you can do that till 15 Sept via the workshop page http://www.bic-gh.de/dwtb2006. Accepted papers will appear in the Journal of Integrative Bioinformatics: http://journal.imbio.de Topics are: + Data Warehouse Development - Architectures - Data integration - Errors and inconsistencies in biological data - Biological ontologies including their quality and consistency - Interfaces for accessing and querying of integrated data - Method integration and analyses in data warehouses + Data Warehouse Applications - Combined dry and wet-lab studies - Sequence and expression data analysis - Regulatory and metabolic networks - Protein-protein interactions - Genotype-phenotype associations - Data and text mining approaches - Workflow management - Computational systems biology The Organising Committee From jeff at bioinformatics.org Thu Jul 13 08:30:46 2006 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 13 Jul 2006 08:30:46 -0400 Subject: [BiO BB] help In-Reply-To: References: <44B3F443.1060806@bioinformatics.org> Message-ID: <44B63CF6.7010903@bioinformatics.org> They may be right, depending on how you'd answer the following questions: 1. One would assume that you're talking about macromolecule (esp. protein) structure when you say "2D to 3D conversion". But, also you say that you're interested in drug design, which indicates that you're talking about *small* molecule structure. Which is it? 2. Does this paper/project/thesis have to be based on novel research that could be published in a refereed journal? Or is it just about anything you're interested in learning? Cheers, Jeff sindhu sambandam wrote: > hi jeff > i'm trying to to do my 6 months project work in software > development...of which i chose to do 2D to 3D conversion...i've still > not decided not that because being an undergraduate student in > biotechnology i dont know how far its possible...but i'm interested in > working in this area > regarding drug designing...its a part of my curriculum...people told me > its a paper not meant for under graduates...they say its tough and > difficult to understand....thats why i needed someone to guide... -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From aloraine at gmail.com Thu Jul 13 11:04:14 2006 From: aloraine at gmail.com (Ann Loraine) Date: Thu, 13 Jul 2006 10:04:14 -0500 Subject: [BiO BB] Finding introns and exons.. In-Reply-To: References: <44B3F443.1060806@bioinformatics.org> Message-ID: <83722dde0607130804w42626821l999b63e46e8000c7@mail.gmail.com> Greetings Hamid, When I do this, I usually get the data from UCSC Genome Informatics Table Browser as a "GFF" file and write some simple scripts to extract non-redundant exons and introns. You can even use simple Unix utilities (grep, cut, uniq) to do the first steps. Fruit fly is actually a good choice for this because the FlyBase gene structure annotations are relatively non-redundant - that is, the same general gene structure is rarely included multiple times, unlike for other data sets from other species. However, in the past I have noticed that when multiple ORFs are associated with a gene structure, FlyBase reports the gene structure multiple times, once per ORF. Also, you have to be careful to filter out pseudogenes and RNA genes, if these are not of interest. Cheers, Ann On 7/13/06, hamid wrote: > Hi buddy, > I need to extract all introns and exons of an organism such as D. > melanogaster. > How can I download all of the introns and exons as a bunch? > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Ann Loraine Assistant Professor Section on Statistical Genetics University of Alabama at Birmingham http://www.ssg.uab.edu http://www.transvar.org From bhakti.dwivedi at gmail.com Thu Jul 13 12:37:51 2006 From: bhakti.dwivedi at gmail.com (Bhakti Dwivedi) Date: Thu, 13 Jul 2006 12:37:51 -0400 Subject: [BiO BB] statistics for prokaryotic genomes Message-ID: Hello everyone, Does anyone know where to find the statistics in general for a prokaryotic genome. I am looking for the parameters such as rate of substitution, transition transversion rate ratio and GC content for the photosynthetic prokaryotic genomes. I found the GC content, but somehow I could't locate the other two parameters. If anybody know the database or publications that has the information about the parameters (the one that I mentioned above) of a prokaryotic genome in general, please let me know. I would really appreciate it. Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From pjain at xldb.di.fc.ul.pt Thu Jul 13 13:11:28 2006 From: pjain at xldb.di.fc.ul.pt (Pooja Jain) Date: Thu, 13 Jul 2006 18:11:28 +0100 Subject: [BiO BB] Native Conformation vs Minimum Energy In-Reply-To: <83722dde0607130804w42626821l999b63e46e8000c7@mail.gmail.com> References: <44B3F443.1060806@bioinformatics.org> <83722dde0607130804w42626821l999b63e46e8000c7@mail.gmail.com> Message-ID: <1152810688.44b67ec0367a5@webservices.di.fc.ul.pt> Dear All, Is it possible that the biological active native state of a protein need not to be of lowest free energy ? -Pooja From baran at genostat.com Sat Jul 15 15:00:58 2006 From: baran at genostat.com (Bob Baran) Date: Sat, 15 Jul 2006 12:00:58 -0700 (PDT) Subject: [BiO BB] need co-instructor for a seminar in Seoul Message-ID: <20060715190058.35168.qmail@web33408.mail.mud.yahoo.com> Needed: Co-instructor for a graduate seminar on genomic signal processing at a major university in Seoul, Korea, during November-December 2006. Travel, housing, and salary will be paid to an inter-disciplinary researcher. The course description (below) is flexible. If interested, contact Robert Baran, or , for more details. Mathematical methods that were developed for communications, speech and signal processing have been adapted to computational biology. Information theory, digital filters, correlation-based methods, spectral analysis, Hidden Markov models, neural networks, support vector machines, blind source separation techniques and many others now find useful applications in the new science of functional genomics and the emerging technology of systems biology. In this seminar, students will survey these applications, learn the basic terminology and paradigms of bioinformatics, focus on selected topics, and gain a clearer understanding of essential signal processing algorithms by applying them to the analysis of molecular sequence and high-throughput data acquired from public sources. The seminar will be conducted in English. From boris.steipe at utoronto.ca Thu Jul 13 15:55:07 2006 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Thu, 13 Jul 2006 15:55:07 -0400 Subject: [BiO BB] Native Conformation vs Minimum Energy In-Reply-To: <1152810688.44b67ec0367a5@webservices.di.fc.ul.pt> References: <44B3F443.1060806@bioinformatics.org> <83722dde0607130804w42626821l999b63e46e8000c7@mail.gmail.com> <1152810688.44b67ec0367a5@webservices.di.fc.ul.pt> Message-ID: <2D921CDF-1B24-4AB8-B744-9C3E8E18F98C@utoronto.ca> If that were the case, one would need to have a large enough energy barrier between the native state and the minimum energy state AND one would need to specify the folding pathway kinetically (the native state is reached faster than the minimum), rather than thermodynamically (the native state is the minimum and all folding trajectories ultimately find it). No, we don't believe this is the way it works in general since this would require specifying and maintaining information in a sequence that is not actually useful. But exceptions are of course "possible", even though to my knowledge none have been rigorously demonstrated. (The example of a protein that folds as a pro-protein but is functional after cleaving the pro-sequence comes close though). HTH Boris On 13-Jul-06, at 1:11 PM, Pooja Jain wrote: > Dear All, > > > Is it possible that the biological active native state of a protein > need not to > be of lowest free energy ? > > -Pooja > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From lichunjiang at sibs.ac.cn Thu Jul 13 21:05:41 2006 From: lichunjiang at sibs.ac.cn (lichunjiang) Date: Fri, 14 Jul 2006 09:05:41 +0800 (CST) Subject: [BiO BB] statistics for prokaryotic genomes In-Reply-To: References: Message-ID: <3926.10.10.224.29.1152839141.squirrel@webmail.sibs.ac.cn> hi, There's a codon usage database online: http://www.kazusa.or.jp/codon/A.html Do you use this for GC content search? Cheers, Lichun Bhakti Dwivedi wrote: > Hello everyone, > > Does anyone know where to find the statistics in general for a prokaryotic > genome. I am looking for the parameters such as rate of substitution, > transition transversion rate ratio and GC content for the photosynthetic > prokaryotic genomes. I found the GC content, but somehow I could't locate > the other two parameters. If anybody know the database or publications > that > has the information about the parameters (the one that I mentioned above) > of > a prokaryotic genome in general, please let me know. I would really > appreciate it. > > Thanks! > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- lichunjiang at sibs.ac.cn Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From hararid at bgu.ac.il Sun Jul 16 05:48:53 2006 From: hararid at bgu.ac.il (Daniel Harari) Date: Sun, 16 Jul 2006 11:48:53 +0200 Subject: [BiO BB] Looking for heat map Software In-Reply-To: References: Message-ID: <44BA0B85.5040003@bgu.ac.il> Hi, I am looking for software that will produce good quality heat maps out of tabular data. The program does not necessarily have to be freeware, although hopefully it will not be too expensive to purchase (such as is the case for SpotFire). I have tried using "R", but the output graphics seem to be pretty awful. Any suggestions would be much appreciated. Daniel From vidyakothekar at yahoo.com Fri Jul 14 07:43:49 2006 From: vidyakothekar at yahoo.com (vidya kothekar) Date: Fri, 14 Jul 2006 04:43:49 -0700 (PDT) Subject: [BiO BB] Native Conformation vs Minimum Energy In-Reply-To: <1152810688.44b67ec0367a5@webservices.di.fc.ul.pt> Message-ID: <20060714114349.8699.qmail@web31310.mail.mud.yahoo.com> Although globular proteins are quite sterdy, and their overall shapes remain same, there may be movement of active site residues, and neighbouring helices. Best way is to compare crystal structures of proteins bound with ligands, if available or do molecular dynamics simulation and compute free energy of interaction V.Kothekar Pooja Jain wrote: Dear All, Is it possible that the biological active native state of a protein need not to be of lowest free energy ? -Pooja _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Dr. Mrs. Vidya Kothekar Res: Flat No. 19, Conifer, Marutrao Gayakwad Nagar D.P. Road, Aundh, Pune 411007, Maharashtra, India Tel 91-20-25887025, 919850532443 e-mail kothekar at hotmail.com vidyakothekar at yahoo.com --------------------------------- Do you Yahoo!? Next-gen email? Have it all with the all-new Yahoo! Mail Beta. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahef111 at link.net Fri Jul 14 17:24:49 2006 From: mahef111 at link.net (mahmoud Elhefnawi) Date: Fri, 14 Jul 2006 21:24:49 -0000 Subject: [BiO BB] re: protein native state Message-ID: <01d001c09634$b65651b0$d098c952@pclr45cvgdscgv> Dear, At least this is true for RNA structures! Mahmoud -------------- next part -------------- An HTML attachment was scrubbed... URL: From bader at cbio.mskcc.org Sun Jul 16 09:51:58 2006 From: bader at cbio.mskcc.org (Gary Bader) Date: Sun, 16 Jul 2006 09:51:58 -0400 Subject: [BiO BB] Looking for heat map Software In-Reply-To: <44BA0B85.5040003@bgu.ac.il> References: <44BA0B85.5040003@bgu.ac.il> Message-ID: <44BA447E.9040507@cbio.mskcc.org> Have you tried Java Treeview? http://jtreeview.sourceforge.net/ Screenshots: http://jtreeview.sourceforge.net/examples/index.html Gary Daniel Harari wrote: > Hi, > > I am looking for software that will produce good quality heat maps out > of tabular data. > The program does not necessarily have to be freeware, although hopefully > it will not be too expensive to purchase (such as is the case for > SpotFire). > I have tried using "R", but the output graphics seem to be pretty awful. > > Any suggestions would be much appreciated. > > Daniel > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- http://baderlab.org Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto From naseebkhan_kakar2003 at yahoo.com Wed Jul 19 01:56:42 2006 From: naseebkhan_kakar2003 at yahoo.com (naseeb kakar2003) Date: Tue, 18 Jul 2006 22:56:42 -0700 (PDT) Subject: [BiO BB] MPhil Bioinformatics in INDIA Message-ID: <20060719055642.28152.qmail@web34402.mail.mud.yahoo.com> Asalma o Alakum i am Mr naseeb Khan from pakistan Sir i need some information redgarding asddmissin in m Phil in ifn bioinformatics. Tanks Naseeb Khan --------------------------------- Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2?/min or less. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sankar.achuth at gmail.com Wed Jul 19 09:56:53 2006 From: sankar.achuth at gmail.com (Dr. Achuthsankar S. Nair) Date: Wed, 19 Jul 2006 19:26:53 +0530 Subject: [BiO BB] MPhil Bioinformatics in INDIA In-Reply-To: <20060719055642.28152.qmail@web34402.mail.mud.yahoo.com> References: <20060719055642.28152.qmail@web34402.mail.mud.yahoo.com> Message-ID: <2b168b460607190656m5da7b952h6c00963f54495026@mail.gmail.com> Dear Naseeb, I just mailed you the details Achuth On 7/19/06, naseeb kakar2003 wrote: > > Asalma o Alakum > i am Mr naseeb Khan from pakistan Sir i need some information redgarding > asddmissin in m Phil in ifn bioinformatics. > Tanks Naseeb Khan > > ------------------------------ > Yahoo! Messenger with Voice. Make PC-to-Phone Callsto the US (and 30+ countries) for 2?/min or less. > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -- Dr Achuthsankar S Nair Hon. Director Centre for Bioinformatics University of Kerala, Trivandrum 695581, INDIA Tel (O) 471-2412759 (R) 471-2542220 www.cbi.keralauniversity.edu www.achu.keralauniversity.edu =================================================================== Admissions to MPhil Bioinformatics for Jan 2007 Open - Brochure and Application forms can be downloaded from www.cbi.keralauniversity.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng.hu at case.edu Thu Jul 20 11:55:05 2006 From: meng.hu at case.edu (Meng Hu) Date: Thu, 20 Jul 2006 11:55:05 -0400 Subject: [BiO BB] Genomes for yeast Message-ID: <94d6903b0607200855t67ca0f33md6b93c654ea27703@mail.gmail.com> Hi, all Can anybody tell me where to find the genome sequences for yeast, such as s. castellii, s. bayanus, etc. I want sth. like the ptt file on ftp://ftp.ncbi.nih.gov/genomes/. I just couldn't find them from the NCBI website. BTW: Where can I find the COG classifications of the genes in these yeast genomes? Thanks in advance. - Meng From karen.morris at bbsrc.ac.uk Thu Jul 20 09:11:12 2006 From: karen.morris at bbsrc.ac.uk (karen morris (RRes-Roth)) Date: Thu, 20 Jul 2006 14:11:12 +0100 Subject: [BiO BB] *** CALL FOR POSTERS AND PARTICIPATION *** Message-ID: Please could the following message be sent to all list members. *** CALL FOR POSTERS AND PARTICIPATION *** 3rd Integrative Bioinformatics Workshop September 4-6, 2006 Rothamsted Research, Harpenden, Hertfordshire, United Kingdom http://www.rothamsted.bbsrc.ac.uk/bab/conf/ibiof/ IMPORTANT DATES (please note that the dates have been revised!!!) August 14: Registration for participation deadline August 21: Poster submission deadline INVITED SPEAKERS Steve Gardner, Chief Technology Officer, Bio wisdom, UK "Semantic Integration, SRS and the Meaning of Life (Sciences)" Gunaretnam Rajagopal, Deputy Director, Bioinformatics Institute, Singapore "BioComputing at Biopolis - Opening New Frontiers at the Interface of Computing, Biology and Medicine" Tom Oinn, Taverna project leader, EBI "Services, Semantics and Workflows in eScience" Pedro Mendes, Virginia Bioinformatics Institute, USA PRELIMINARY PROGRAMME Monday 4th September 2006 11:30 Registration desk opens 12:30 Lunch (buffet style) 13:10 Welcome followed by some administrivia Session 1 - Database Integration and Integrative Databases 13:20 (keynote) Semantic Integration, SRS and the Meaning of Life (Sciences) Steve Gardner (Biowisdom, UK) 14:00 CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes Baumbach, J; Brinkrolf, K; Wittkop, T; Tauch, A; Rahmann, S 14:25 Analysing Microarray Data using the Multi-functional Immune Ontologiser Khalid, S; Fraser, K; Khan, M; Wang, P; Liu, X; Li, S 14:50 The BioRS(TM) Integration and Retrieval System: An open system for distributed data integration Kaps, A; Dyshlevoi, K; Heumann, K; Jost, R; Kontodinas, I; Wolff, M; Hani, J 15:15 Integration of Protein and Protein-Protein Interaction Data: Feasibility Report using Microsoft .NET Stra?er, W; Siegl, D; ?nder, K; Bauer, J 15:40 Coffee break 16:00 BN++ - A Biological Information System K?ntzer, J; Blum, T; Gerasch, A; Backes, C; Hildebrandt, A; Kaufmann, M; Kohlbacher, O; Lenhof, HP 16:25 MILAN - A medical information-system linking agents to metabolic networks Prins, B; Hofest?dt, R 16:50 Data Cleaning and Semantic Improvement in Biological Databases Apiletti, D; Bruno, G; Ficarra, E; Baralis, E 17:15 Drinks and Poster Session Tuesday 5th September 2006 09:30 Coach from recommended hotel Session 2 - Integrative Systems Biology (Modelling and Simulation) 10:00 (keynote) Title to be announced Pedro Mendes (Virginia Bioinformatics Institute, USA) 10:40 Noise in Genetic Toggle Switch Models Andrecut, M; Kauffman, SA 11:05 BASIS: an internet resource for network modelling Gillespie, CS; Wilkinson, DJ; Shanley, DP; Proctor, CJ; Boys, RJ; Kirkwood, TBL 11:30 Coffee break 11:45 Overview of the contributions of the SBML Team to the formalisation and systematic storage of models of biochemical reaction networks. Keating, SM; Bornstein, BJ; Finney, A; Hucka, M 12:10 The implications for Bioinformatics of integration across physical scales Hodgman, TC; Ugartechea-Chirino, Y; Tansley, G; Dryden, I 12:35 A Graphical Notation to Describe the Logical Interactions of Biological Pathways Moodie, SL; Sorokin, A; Goryanin, I; Ghazal, P 13:00 Exact and Approximate Stochastic Simulations of the MAPK Pathway and Comparisons of Simulations' Results Purutcuoglu, V; Wit, E 13:25 Lunch (buffet style) Session 3 Integrative Systems Biology (Networks) 14:20 keynote BioComputing at Biopolis - Opening New Frontiers at the Interface of Computing, Biology and Medicine Gunaretnam Rajagopal (Bioinformatics Institute, Singapore) 15:00 Statistical Embedding in Complex Biosystems Capobianco, E 15:25 An assessment of machine and statistical learning approaches to inferring networks of protein-protein interactions Azuaje, F 15:50 Multi-model inference of network properties from incomplete data Stumpf, MPH; Thorne, T 16:15 Coffee break Session 4 Data Analysis and Interpretation (Transcriptomics) 16:30 Co-expressed gene groups analysis (CGGA): An automatic tool for the interpretation of microarray experiments Martinez, R; Pasquier, N; Collard, M; Lopez, L; Pasquier, C 16:55 Combining biomedical knowledge and transcriptomic data to extract new knowledge on genes Gu?rin, E; Marquet, G; Chabalier, J; Troadec, M-B; Guguen-Guillouzo, C; Lor?al, O; Burgun, A; Moussouni, F 17:20 Inference of Gene Coexpression Networks by Integrative Analysis across Microarray Experiments Elo, LL; Lahesmaa, R; Aittokallio, T 17:45 Modelling Microarray Data: Interpreting and communicating the biological results Pittelkow, YE; Wilson, SR 18:10 Targeted Projection Pursuit Tool for Gene Expression Visualisation Faith, J; Brockway, M 18:35 Poster session and Bar opens 19:30 Conference dinner Wednesday 6th September 2006 09:30 Coach from recommended hotel Session 5 Data Analysis and Interpretation 10:00 (keynote) Services, Semantics and Workflows in eScience Tom Oinn (European Bioinformatics Institute, UK) 10:40 Metabolite profiles as a reflection of physiological status - a methodological validation Steinfath, M; Repsilber, D; Hische, M; Schauer, N; Fernie, A; Selbig, J 11:05 A First Step towards Learning which uORFs Regulate Gene Expression Selpi, S; Bryant, CH; Kemp, GJL; Cvijovic, M 11:30 Coffee break 11:50 Prediction of transcription factor binding to DNA using rule induction methods Huss, M; Nordstr?m, K 12:15 Functional diversity within protein superfamilies Casbon, J; Saqi, M 12:40 Closing remarks 12:50 Lunch (buffet style) Depart ORGANISING COMMITTEE Julio Collado-Vides UNAM, Mexico Ralf Hofest?dt Bielefeld University, Germany Paul Kersey EBI, UK Jacob Koehler RRes, UK Chris Rawlings RRes, UK Uwe Scholz IPK Gatersleben, Germany Paul Verrier RRes, UK CONTACT Karen Morris, BAB Division, Rothamsted Research, West Common, Harpenden, Herts. AL5 2JQ, UK karen.morris at bbsrc.ac.uk tel: 01582 763133 ext 2813 fax: 01582 467907 From wilfred at sdsc.edu Thu Jul 20 12:57:12 2006 From: wilfred at sdsc.edu (Wilfred Li) Date: Thu, 20 Jul 2006 09:57:12 -0700 Subject: [BiO BB] Genomes for yeast In-Reply-To: <94d6903b0607200855t67ca0f33md6b93c654ea27703@mail.gmail.com> Message-ID: <452F37AE49199D49B1702D7D45038C4D6B0695@et.ad.sdsc.edu> How about the NCBI Genome Project site http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj Looks like S. castellii is still in draft assembly. So probably no COG classification has been done for these yet. Here are all the genomes in the current version of COG: http://www.ncbi.nlm.nih.gov/COG/new/orgs.html#Eukaryota Regards, Wilfred -----Original Message----- From: bio_bulletin_board-bounces+wilfred=sdsc.edu at bioinformati cs.org [mailto:bio_bulletin_board-bounces+wilfred=sdsc.edu at bioi nformatics.org] On Behalf Of Meng Hu Sent: Thursday, July 20, 2006 8:55 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Genomes for yeast Hi, all Can anybody tell me where to find the genome sequences for yeast, such as s. castellii, s. bayanus, etc. I want sth. like the ptt file on ftp://ftp.ncbi.nih.gov/genomes/. I just couldn't find them from the NCBI website. BTW: Where can I find the COG classifications of the genes in these yeast genomes? Thanks in advance. - Meng _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From maximilianh at gmail.com Sat Jul 22 20:49:14 2006 From: maximilianh at gmail.com (Maximilian Haeussler) Date: Sun, 23 Jul 2006 02:49:14 +0200 Subject: [BiO BB] Looking for heat map Software In-Reply-To: <44BA0B85.5040003@bgu.ac.il> References: <44BA0B85.5040003@bgu.ac.il> Message-ID: <76f031ae0607221749o58f02109h9389cb8971449ba@mail.gmail.com> Hi, what do you find awful about the R heatmap? http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=66 max On 16/07/06, Daniel Harari wrote: > Hi, > > I am looking for software that will produce good quality heat maps out > of tabular data. > The program does not necessarily have to be freeware, although hopefully > it will not be too expensive to purchase (such as is the case for > SpotFire). > I have tried using "R", but the output graphics seem to be pretty awful. > > Any suggestions would be much appreciated. > > Daniel > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From hararid at bgu.ac.il Sun Jul 23 02:31:04 2006 From: hararid at bgu.ac.il (Daniel Harari) Date: Sun, 23 Jul 2006 08:31:04 +0200 Subject: [BiO BB] Looking for heat map Software In-Reply-To: <76f031ae0607221749o58f02109h9389cb8971449ba@mail.gmail.com> References: <"44B A0B85.5040003"@bgu.ac.il> <76f031ae0607221749o58f02109h9389cb8971449ba@mail.gmail.com> Message-ID: <44C317A8.5040908@bgu.ac.il> Hi Max, Thanks for responding. I am new to writing R scripts and am not sure if I can overcome a few obstacles. Do you know the answer to these questions? - Do you know of a way to generate a user-defined upper and lower range in which to define the color-code of the heatmap? - R also offers a number of pseudocolor options, but in my output files, I always see the same pink-green-white output. Thanks, Daniel Maximilian Haeussler wrote: > Hi, > > what do you find awful about the R heatmap? > http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=66 > > max > > On 16/07/06, Daniel Harari wrote: > >> Hi, >> >> I am looking for software that will produce good quality heat maps out >> of tabular data. >> The program does not necessarily have to be freeware, although hopefully >> it will not be too expensive to purchase (such as is the case for >> SpotFire). >> I have tried using "R", but the output graphics seem to be pretty awful. >> >> Any suggestions would be much appreciated. >> >> Daniel >> _______________________________________________ >> Bioinformatics.Org general forum - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Daniel Harari, Ph.D. Rubin Lab. National Institute for Biotechnology in the Negev Building 39, room -113 Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Email: hararid at bgu.ac.il Tel: 08-6477180 Fax: 08-6472983 From akarger at CGR.Harvard.edu Mon Jul 24 10:06:46 2006 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Mon, 24 Jul 2006 10:06:46 -0400 Subject: [BiO BB] RE: Genomes for yeast Message-ID: > From: "Meng Hu" > > Hi, all > > Can anybody tell me where to find the genome sequences for > yeast, such as > s. castellii, s. bayanus, etc. Jason Stajich of bioperl fame has a bunch of good stuff consolidated at http://fungal.genome.duke.edu/ You'll have to parse the GFF or other files to get the details, though, AFAIK. - Amir Karger Research Computing Bauer Center for Genomics Research Harvard University 617-496-0626 From rrwagner at faw.uni-linz.ac.at Sun Jul 23 11:01:55 2006 From: rrwagner at faw.uni-linz.ac.at (Prof.Roland Wagner) Date: Sun, 23 Jul 2006 17:01:55 +0200 Subject: [BiO BB] Call for Papers Bird Message-ID: <44C38F63.2060403@faw.uni-linz.ac.at> *CALL FOR PAPERS* * * *and* * * *CALL FOR POSTERS* * * *1st International Conference* *on* * * *Bioinformatics Research and Development* * B I R D '07* *http://www.birdconf.org* * * *Berlin**, Germany*** *March 12-14, 2007* * * * * *Keynote Talk: * * * *Josef Penninger* Institute of Molecular Biotechnology (IMBA) * * *Scope of the conference:* * * The primary focus of BIRD '07 is to provide researchers and users in the field of bioinformatics a forum in which to interact about new research directions, developments, and software/web services. It encompasses the methods of solving biological, medical, or chemical problems by computer science, machine learning, or information processing tools. The conceptual level of the methods range from theoretical approaches through the design of algorithms, models, and information processing systems through to the development of software packages and web services. The program committee seeks contributions, which topics include, but are not limited to: * * * Algebraic Biology * Databases & Data Integration * Drug Design * Ontologies & Textmining * Evolution and Phylogenetics * Genomics * Gene and Splice Site Recognition * Machine Learning and Data Analysis * Gene Expression/Regulation & Microarrays * MicroRNA and RNAi * Molecular Diagnostics and Treatment Support * Molecular Dynamics * Pathways, Networks, Systems Biology * Phylogenetics & Molecular Evolution * Protein & RNA Structure and Function * Proteomics * Sequence Analysis & Alignment * SNPs and Haplotyping * Systems Biology and Modelling * * *General Chair:* Roland Wagner, FAW, University of Linz, Austria *Program Chair:* Sepp Hochreiter, University of Linz, Austria * * *Program Committee (Steering):* Amos Bairoch, Swiss Institute of Bioinformatics, Switzerland Pierre Baldi, University of California, Irvine, USA Philip E. Bourne, UCSD, USA Cornelius Fr?mmel, Georg-August-Universit?t G?ttingen, Germany David Gilbert, University of Glasgow, UK Amarnath Gupta, SDSC of the University of California San Diego, USA Knut Reinert, FU Berlin, Germany Burkhard Rost, Columbia University, USA Hershel Safer, Weizmann Institute of Science, Israel Erik Sonnhammer, Karolinska Institute, Sweden and about 200 other PC-members * * *Paper Submission Details: *Authors are invited to submit original research contributions or experience reports in English. Paper registration and electronic submission will start in August 2006. Submitted papers will be carefully evaluated based on originality, significance, technical soundness, and clarity of exposition. *Important Dates:* * Submission of Full Papers: September 8, 2006 * Noification of Acceptance: November 20, 2006 * Camera-ready Copies of papers: December 20, 2006 For further inquiries, please contact: Prof. Dr. Sepp Hochreiter, Institute of Bioinformatics, University of Linz, A-4040 Linz, Austria, or the BIRD Conference Organisation Office (office at birdconf.org ) *All accepted conference papers will be published in "Lecture Notes in Bioinformatics" (LNBI) by Springer Verlag.* -- Univ. Prof. Dr. Roland Wagner Director of the Institute of Applied Knowledgeprocessing (FAW) Director of the Institute "integriert studieren" Tel.: +43 676 84673210 Fax: +43 732 24689308 rrwagner at faw.uni-linz.ac.at sec1: Monika Neubauer Tel.: +43 676 84673212 Fax.:+43 732 2468 9308 mneubauer at faw.uni-linz.ac.at sec2: Barbara Arrer Tel: +43 732 2468 9232 Fax:+43 732 2468 9322 barbara.arrer at jku.ta http://www.faw.uni-linz.ac.at http://www.integriert-studieren.jku.at http://www.dexa.org http://www.icchp.org From frcerqueira at gmail.com Tue Jul 25 09:13:18 2006 From: frcerqueira at gmail.com (Fabio Cerqueira) Date: Tue, 25 Jul 2006 15:13:18 +0200 Subject: [BiO BB] Mass spec output Message-ID: <50fceb2c0607250613k1a1da07fh832c3ab739f605bf@mail.gmail.com> Hi there, Does anyone know a good source describing details about mzData files concerning the kind of information this sort of file contains? Actually I am interested in having detailed description about all kind of information that is contained in the output of a mass spectrometer. Thus, I was thinking in analysing a very used data format like mzData to figure it out, but I am open to another kind of source that could provide the information I need. Thanks, Fabio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From joets at moulon.inra.fr Tue Jul 25 10:55:21 2006 From: joets at moulon.inra.fr (Johann JOETS) Date: Tue, 25 Jul 2006 16:55:21 +0200 Subject: [BiO BB] Mass spec output In-Reply-To: <50fceb2c0607250613k1a1da07fh832c3ab739f605bf@mail.gmail.com> Message-ID: <007001c6affa$59e12550$3372668a@Bioinfo1> Dear Fabio, The whole information is there : http://psidev.sourceforge.net/ Unfortunately, the site seems to be partly down at this time. However you will find some sample files to download (http://sourceforge.net/project/showfiles.php?group_id=65472). You may also have a look at the mzXML http://www.proteomecenter.org/software.php. A fusion of the PSI and the Seattle proteome center schemata is planned. Therefore these formats may not considered as fully stable yet. Hope this will help J Joets -----Message d'origine----- De : bio_bulletin_board-bounces+joets=moulon.inra.fr at bioinformatics.org [mailto:bio_bulletin_board-bounces+joets=moulon.inra.fr at bioinformatics.o rg] De la part de Fabio Cerqueira Envoy? : mardi 25 juillet 2006 15:13 ? : bio_bulletin_board at bioinformatics.org Objet : [BiO BB] Mass spec output Hi there, Does anyone know a good source describing details about mzData files concerning the kind of information this sort of file contains? Actually I am interested in having detailed description about all kind of information that is contained in the output of a mass spectrometer. Thus, I was thinking in analysing a very used data format like mzData to figure it out, but I am open to another kind of source that could provide the information I need. Thanks, Fabio. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgw106 at york.ac.uk Tue Jul 25 12:55:59 2006 From: dgw106 at york.ac.uk (DGW) Date: Tue, 25 Jul 2006 17:55:59 +0100 Subject: [BiO BB] rpsblast error codes Message-ID: <44C64D1F.1080708@york.ac.uk> Dear Bio BB list, I have a rather unusual and technical problem regarding rpsblast. I have emailed the NCBI Blast helpdesk, but they have not been able to explain yet, so I'm hoping there is someone with some insider knowledge out there who could help. I am using a python script that runs rpsblast for many queries. At each call of the rpsblast executable, this script requires that rpsblast returns a value of zero to indicate a successful run, before attempting to parse the output and move onto the next query. Unfortunately, rpsblast doesn't return zero, but returns the value '768', even though each search seems to complete perfectly fine. The system being used is a Sun OS5 machine. When I test the script on my laptop (Win XP) using the precompiled binaries for rpsblast it works just fine. I can bypass the problem, by just looking for '768' instead of '0', but this doesn't bode well for the portability of the script. Also, I am curious as to what is causing this to happen. So, does anyone know what the error values for rpsblast stand for (there seems to be no documentation on this)? Are they determined by the source code, or by the system the program is compiled on? Cheers David From erant at psb.ugent.be Thu Jul 27 11:10:29 2006 From: erant at psb.ugent.be (Erick Antezana) Date: Thu, 27 Jul 2006 17:10:29 +0200 Subject: [BiO BB] CfP: I Latin-American Congress of Medical Informatics Message-ID: <3bf67348c3d7217915dbcdc561dcb2a0@psb.ugent.be> CfP: I Latin-American Congress of Medical Informatics ========================================== Authors are invited to submit papers for the I Latin-American Medical Informatics Congress (?Medical Informatics Latin America?). Papers should describe developments, research, or applications related to Medical Informatics and include some or all of the folowing aspects: analysis, design, implementation, usage, and results. Areas ===== Submissions should pertain to one of the following areas: ? Telemedicine ? Bioinformatics ? Information Technology in Medicine ? E-learning in Medicine ? Applications Venue ===== The I Latin-American Congress of Medical Informatics will take place in the city of Cochabamba, the so-called ?garden-city? of Bolivia. Cochabamba is located at an altitude of approximately 2500 m (8500 feet) above sea level. In November, the average daytime temperature is about 26?C (80?F), with an average minimum temperature of 12?C (55?F). The main tourism area of the Chapare can be reached by car within 4 hours. Set within a natural environment and preserving the original vegetation, the USIP campus, where some events will be held, is located at the foot of San Pedro Hill, on the main road to Santa Cruz. To reach downtown from the USIP campus, it takes only about 10 minutes by taxi. Key dates ======== August 14, 2006 Deadline for abstract submission September 5, 2006 Notice of acceptance October 9, 2006 Deadline for whole paper submittal October 20, 2006 Deadline for registration with a discount October 30, 2006 Deadline for final paper submittal (with corrections) November 6, 2006 Registration and opening ceremony November 6 - 9, 2006 Congress November 8 Welcome concert November 9, 2006 Closing ceremony More info ======= Emilio Aliss Vice Rector of Extension Sim?n I. Pati?o University E-mail: e.aliss at usip.edu.bo http://www.usip.edu.bo -------------- next part -------------- A non-text attachment was scrubbed... Name: MILA-2006.pdf Type: application/pdf Size: 90357 bytes Desc: not available URL: From y.itan at ucl.ac.uk Thu Jul 27 12:22:36 2006 From: y.itan at ucl.ac.uk (Yuval Itan) Date: Thu, 27 Jul 2006 17:22:36 +0100 Subject: [BiO BB] Getting sequences by base pair locations Message-ID: <3c0c24306264dfc986eda4dab362215f@ucl.ac.uk> Hello all, I was BLATing a few hundred human genes against the chimp genome, and kept the best chimp hits for every human gene. I have the base pair start and end location for every chimp hit, and I need to get the sequence for each of these chimp hits. Here is an example for a few chimp hits bp locations: Start End 142854 144504 154479 155198 153066 167370 163146 163559 I have one chimp genome file (about 3GB) including all chromosomes, but I could also get one file per chromosome if that would make things easier. Does anyone have a script or a link for an interface that can do the job? Thank you very much, Yuval -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 843 bytes Desc: not available URL: From Daniele.Santoni at caspur.it Fri Jul 28 07:38:45 2006 From: Daniele.Santoni at caspur.it (Daniele Santoni) Date: Fri, 28 Jul 2006 13:38:45 +0200 Subject: [BiO BB] clustalw alignment pairwise Message-ID: <20060728113845.A9B8253690@smtp.caspur.it> Hi everybody, We are aligning a sample sequence with a consensus sequence in order to identify mutations, deletions and insertions. Due to the presence of gaps we lack the correct open reading frame as you can see below (seqA). Can we solve the problem using some options of clustalw? This is an example: cons TTAACCCCACTCTGTGTTACTTTAAATTGCACTGATTTGATGAATGCTACTAATACCAAT 60 seqA TTAACCCCACTCTGTGTTACTTTAAATTGTAATGGCACTCGAAACAGCACTCAAAACAGC 60 ***************************** * ** ** *** * * ** cons ACTACTATAATATATAGATGGAGAGGAGAAATAAAAAACTGCTCTTTCAATATCACCACA 120 seqA ACC-CTGGAA-----GAAAAGTCAGGGACAATACAAAACTGTTCTTTCAATATGACCACA 114 ** ** ** * * *** **** ******* *********** ****** Thank you in advance for every suggestions Best regards Daniele From nuin at terra.com.br Fri Jul 28 08:12:27 2006 From: nuin at terra.com.br (Paulo Nuin) Date: Fri, 28 Jul 2006 08:12:27 -0400 Subject: [BiO BB] clustalw alignment pairwise In-Reply-To: <20060728113845.A9B8253690@smtp.caspur.it> Message-ID: <20060728121202.8F2B73683BF@primary.bioinformatics.org> Hi Isn't one of your first objectives to identify deletions? It seems that you have found one. Most of the alignment looks pretty good to me. What you might try is to use another program and compare the results. HTH Paulo -----Original Message----- From: bio_bulletin_board-bounces+pnuin=terra.com.br at bioinformatics.org [mailto:bio_bulletin_board-bounces+pnuin=terra.com.br at bioinformatics.org] On Behalf Of Daniele Santoni Sent: July 28, 2006 7:39 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] clustalw alignment pairwise Hi everybody, We are aligning a sample sequence with a consensus sequence in order to identify mutations, deletions and insertions. Due to the presence of gaps we lack the correct open reading frame as you can see below (seqA). Can we solve the problem using some options of clustalw? This is an example: cons TTAACCCCACTCTGTGTTACTTTAAATTGCACTGATTTGATGAATGCTACTAATACCAAT 60 seqA TTAACCCCACTCTGTGTTACTTTAAATTGTAATGGCACTCGAAACAGCACTCAAAACAGC 60 ***************************** * ** ** *** * * ** cons ACTACTATAATATATAGATGGAGAGGAGAAATAAAAAACTGCTCTTTCAATATCACCACA 120 seqA ACC-CTGGAA-----GAAAAGTCAGGGACAATACAAAACTGTTCTTTCAATATGACCACA 114 ** ** ** * * *** **** ******* *********** ****** Thank you in advance for every suggestions Best regards Daniele _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board E-mail classificado pelo Identificador de Spam Inteligente Terra. Para alterar a categoria classificada, visite http://mail.terra.com.br/protected_email/imail/imail.cgi?+_u=pnuin&_l=1,1154 087312.556763.17756.caneria.hst.terra.com.br,4595,Des15,Des15 Esta mensagem foi verificada pelo E-mail Protegido Terra. Scan engine: McAfee VirusScan / Atualizado em 27/07/2006 / Vers?o: 4.4.00/4816 Proteja o seu e-mail Terra: http://mail.terra.com.br/ From gary at primary.bioinformatics.org Fri Jul 28 08:29:56 2006 From: gary at primary.bioinformatics.org (Gary Van Domselaar) Date: Fri, 28 Jul 2006 08:29:56 -0400 (EDT) Subject: [BiO BB] clustalw alignment pairwise In-Reply-To: <20060728121202.8F2B73683BF@primary.bioinformatics.org> References: <20060728121202.8F2B73683BF@primary.bioinformatics.org> Message-ID: Hi Daniele, Clustalw doesnt have a provision for preserving reading frame on nucleotide alignments, so what we do is use an 'align on codons' procedure where we do a multiple alignment on the protein translations, then back translate that alignment in to the original nucleotide sequences. The freely downloadable windows-based program 'MEGA3' will do this for you. Regards, g. -- Gary Van Domselaar, PhD Associate Director, Bioinformatics.Org gary at bioinformatics.org From benitov at hotmail.fr Fri Jul 28 10:28:00 2006 From: benitov at hotmail.fr (Benoit Varvenne) Date: Fri, 28 Jul 2006 14:28:00 +0000 Subject: [BiO BB] Difference between Riken cDNA and others ? Message-ID: Hello everybody, I would like to find the relevant difference(s) between a Riken cDNA and the others (reliability ?, way to obtain it ?, source only ?) in order to make a little speech about it but i could find no information on this topic. Can someone help me here ? Thanks a lot, Regards, Beno?t _________________________________________________________________ Ten : profite de ton Messenger en illimit? sur ton mobile ! http://mobile.live.fr/messenger/ten/ From maclwl01 at ipfw.edu Fri Jul 28 11:32:45 2006 From: maclwl01 at ipfw.edu (William Macleod) Date: Fri, 28 Jul 2006 10:32:45 -0500 Subject: [BiO BB] virus taxonomy question Message-ID: <1154100765.8a31799cmaclwl01@ipfw.edu> by what criteria can one judge a virus to be a new strain? bill From MEC at Stowers-Institute.org Fri Jul 28 12:19:42 2006 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Fri, 28 Jul 2006 11:19:42 -0500 Subject: [BiO BB] Getting sequences by base pair locations Message-ID: There are many options. But, it looks like you only have start end coordinates! Where do you know which chromosome/contig the hit was on? Assuming you have this, if you did the blat with a local copy of the blat program and a the genome, then in addition to the blat command, you have the twoBitToFa command which can extract the hits from the blat index (see http://genome.ucsc.edu/goldenPath/help/blatSpec.html) Or did you do the blat at ucsc? Malcolm Cook Database Applications Manager, Bioinformatics Stowers Institute for Medical Research ________________________________ From: bio_bulletin_board-bounces+mec=stowers-institute.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at bioinformat ics.org] On Behalf Of Yuval Itan Sent: Thursday, July 27, 2006 11:23 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Getting sequences by base pair locations Hello all, I was BLATing a few hundred human genes against the chimp genome, and kept the best chimp hits for every human gene. I have the base pair start and end location for every chimp hit, and I need to get the sequence for each of these chimp hits. Here is an example for a few chimp hits bp locations: Start End 142854 144504 154479 155198 153066 167370 163146 163559 I have one chimp genome file (about 3GB) including all chromosomes, but I could also get one file per chromosome if that would make things easier. Does anyone have a script or a link for an interface that can do the job? Thank you very much, Yuval From MEC at Stowers-Institute.org Fri Jul 28 12:41:21 2006 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Fri, 28 Jul 2006 11:41:21 -0500 Subject: [BiO BB] clustalw alignment pairwise Message-ID: Daniele, Depending on how often you do this, and your computational and financial resources, and what platforms you are comfortable with, you might reconsider your approach. I particular, I recommend that you consider to use Staden for your project (http://staden.sourceforge.net/). It uses Gap4 or phrap under the hood for assembly purposes, provides a few deffernt methods for automatically scoring mutations (http://staden.sourceforge.net/mutations/index.html), provides a gui to view and curate the (sometimes incorrect) scoring in the context of the actual traces, and provides a standard output format for reporting the mutations that takes the ORF of a reference sequence into account for reporting the consequence of the mutation in both html (http://staden.sourceforge.net/mutations/index_short.html) and text format, like this: 001321_11aF 33885T>Y (silent F) (strand - only) 001321_11aF 34407G>K (expressed E>[ED]) (strand - only) 001321_11cF 35512T>Y (silent L) (double stranded) 001321_11cF 35813C>Y (expressed P>[PL]) (double stranded) 001321_11dF 36314A>R (expressed E>[EG]) (double stranded) 001321_11eF 36749A>R (expressed K>[KR]) (double stranded) 001321_11eF 37313T>K (noncoding) (strand - only) 000256_11eF 36749A>G (expressed K>R) (double stranded) (above from http://staden.sourceforge.net/mutations/index.html) I've used it to good effect for all the above. Regards, Malcolm Cook Database Applications Manager, Bioinformatics Stowers Institute for Medical Research >-----Original Message----- >From: >bio_bulletin_board-bounces+mec=stowers-institute.org at bioinforma >tics.org >[mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at bi >oinformatics.org] On Behalf Of Daniele Santoni >Sent: Friday, July 28, 2006 6:39 AM >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] clustalw alignment pairwise > >Hi everybody, > >We are aligning a sample sequence with a consensus sequence in >order to >identify mutations, deletions and insertions. >Due to the presence of gaps we lack the correct open reading >frame as you >can see below (seqA). Can we solve the problem using some options of >clustalw? > >This is an example: >cons TTAACCCCACTCTGTGTTACTTTAAATTGCACTGATTTGATGAATGCTACTAATACCAAT 60 >seqA TTAACCCCACTCTGTGTTACTTTAAATTGTAATGGCACTCGAAACAGCACTCAAAACAGC 60 > ***************************** * ** ** *** * * ** > >cons ACTACTATAATATATAGATGGAGAGGAGAAATAAAAAACTGCTCTTTCAATATCACCACA 120 >seqA ACC-CTGGAA-----GAAAAGTCAGGGACAATACAAAACTGTTCTTTCAATATGACCACA 114 > ** ** ** * * *** **** ******* *********** ****** > >Thank you in advance for every suggestions > >Best regards > >Daniele >_______________________________________________ >Bioinformatics.Org general forum - >BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From chea at mail.nih.gov Fri Jul 28 15:49:50 2006 From: chea at mail.nih.gov (Che, Anney (NIHNIAID)) Date: Fri, 28 Jul 2006 15:49:50 -0400 Subject: [BiO BB] Automate local NCBI database updating Message-ID: Hi, I would like to download a local NCBI database and automate the database update nightly. Could any one tell me where I can find instruction how to do this. Thanks in advance, Anney -- From liangyou at gmail.com Sat Jul 29 18:06:03 2006 From: liangyou at gmail.com (Liangyou) Date: Sat, 29 Jul 2006 18:06:03 -0400 Subject: [BiO BB] Getting sequences by base pair locations In-Reply-To: <3c0c24306264dfc986eda4dab362215f@ucl.ac.uk> References: <3c0c24306264dfc986eda4dab362215f@ucl.ac.uk> Message-ID: What do you want to automate? The whole process including: blasting all sequences from a database of sequences, getting the start and end positions of the best hits, and getting the sequence for each hit? Or just want to get the sequence for each hit? If you want to do the whole process and you know how to get the sequence for each hit (either from a Web interface, or you have a standalone program to extract the sequence from the genome) I may help you to set up a script. It is just needs a couple of hours to do so. Yours, Liangyou On 7/27/06, Yuval Itan wrote: > Hello all, > > I was BLATing a few hundred human genes against the chimp genome, and > kept the best chimp hits for every human gene. > I have the base pair start and end location for every chimp hit, and I > need to get the sequence for each of these chimp hits. Here is an > example for a few chimp hits bp locations: > > Start End > 142854 144504 > 154479 155198 > 153066 167370 > 163146 163559 > > I have one chimp genome file (about 3GB) including all chromosomes, but > I could also get one file per chromosome if that would make things > easier. Does anyone have a script or a link for an interface that can > do the job? > > Thank you very much, > > Yuval > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > From hershel.safer at weizmann.ac.il Sun Jul 30 08:18:35 2006 From: hershel.safer at weizmann.ac.il (Hershel Safer) Date: Sun, 30 Jul 2006 15:18:35 +0300 Subject: [BiO BB] DATE CHANGE - European Conf. on Computational Biology (ECCB) Message-ID: <44CCA39B.3080309@weizmann.ac.il> We appreciate the concern that some people have expressed regarding the security situation in Israel and how it will affect the safety of participants in the 5th European Conference on Computational Biology (ECCB ?06). In order to host a high-quality conference that people will feel comfortable attending, we are delaying the conference to January 21-24, 2007. The conference schedule will remain unchanged to the greatest extent possible. We are in the process of contacting all the speakers to verify that they will be able to participate on the new dates. The scientific program is available for viewing on the web at www.eccb06.org , and any changes will be displayed there. Many people will have achieved new results during the intervening months. We are planning an additional session for presenting late-breaking results; we will send an announcement once the details have been worked out. We realize that some people have already made travel plans, and in particular may have to pay penalties to reschedule their airline tickets. Travel to Eilat should be somewhat less expensive in January than in September, which should help offset the change fee. In addition, hotel prices will be approximately 10% lower; detailed prices will be posted on the website when they are available. Overall, the change in dates should have at most a small effect on the cost of participation. People who have already registered for the conference can simply maintain their reservations, and hotel reservations made via the conference website will be moved to the corresponding dates in January; confirmations will be sent shortly. The early-registration deadline will be extended to Tuesday, November 21, 2006. Anybody who has already registered at the regular registration rate will be charged only the early-registration fee. The new dates will, unfortunately, be inconvenient for some people who planned to participate in September. Cancellations received by August 31, 2006, will be processed without a cancellation fee. Thereafter, the standard policy will apply; cancellations until three weeks before the start of the conference will be charged a $30 processing fee. The weather in Eilat is very pleasant in January, averaging 22C (72F). Always pleasant as a Red Sea resort, Eilat is especially attractive during the northern-hemisphere winter months. Eilat itself is safe, both in terms of street crime and terrorist activity. Travel from Ben Gurion International Airport to Eilat is also safe and has been continuing without interruption. The post-conference tours go only to safe areas. Details about matters related to the date change are being added to the FAQ page on the conference website. Please contact the Secretariat (eccb06 at diesenhaus.com) if you have questions that are not answered in the FAQ. We apologize that events beyond our control have caused us to change the conference dates and for the inconvenience that this will cause you. We nevertheless look forward to seeing you in Eilat for an exciting conference in January 2007! Best regards, Hershel Safer and Haim Wolfson ECCB Conference Chairs From sswang at berkeley.edu Mon Jul 31 13:02:38 2006 From: sswang at berkeley.edu (Sarah Wang) Date: Mon, 31 Jul 2006 10:02:38 -0700 Subject: [BiO BB] DATE CHANGE - European Conf. on Computational Biology (ECCB) In-Reply-To: <44CCA39B.3080309@weizmann.ac.il> Message-ID: Do you still accept poster presentations if the meeting date is changed? I'm interested in a poster presentation at the conference, if it's held in January. Best Sarah On 7/30/06 5:18 AM, "Hershel Safer" wrote: > We appreciate the concern that some people have expressed regarding the > security situation in Israel and how it will affect the safety of > participants in the 5th European Conference on Computational Biology > (ECCB ?06). In order to host a high-quality conference that people will > feel comfortable attending, we are delaying the conference to January > 21-24, 2007. > > The conference schedule will remain unchanged to the greatest extent > possible. We are in the process of contacting all the speakers to verify > that they will be able to participate on the new dates. The scientific > program is available for viewing on the web at www.eccb06.org > , and any changes will be displayed there. > > Many people will have achieved new results during the intervening > months. We are planning an additional session for presenting > late-breaking results; we will send an announcement once the details > have been worked out. > > We realize that some people have already made travel plans, and in > particular may have to pay penalties to reschedule their airline > tickets. Travel to Eilat should be somewhat less expensive in January > than in September, which should help offset the change fee. In addition, > hotel prices will be approximately 10% lower; detailed prices will be > posted on the website when they are available. Overall, the change in > dates should have at most a small effect on the cost of participation. > > People who have already registered for the conference can simply > maintain their reservations, and hotel reservations made via the > conference website will be moved to the corresponding dates in January; > confirmations will be sent shortly. > > The early-registration deadline will be extended to Tuesday, November > 21, 2006. Anybody who has already registered at the regular registration > rate will be charged only the early-registration fee. > > The new dates will, unfortunately, be inconvenient for some people who > planned to participate in September. Cancellations received by August > 31, 2006, will be processed without a cancellation fee. Thereafter, the > standard policy will apply; cancellations until three weeks before the > start of the conference will be charged a $30 processing fee. > > The weather in Eilat is very pleasant in January, averaging 22C (72F). > Always pleasant as a Red Sea resort, Eilat is especially attractive > during the northern-hemisphere winter months. > > Eilat itself is safe, both in terms of street crime and terrorist > activity. Travel from Ben Gurion International Airport to Eilat is also > safe and has been continuing without interruption. The post-conference > tours go only to safe areas. > > Details about matters related to the date change are being added to the > FAQ page on the conference website. Please contact the Secretariat > (eccb06 at diesenhaus.com) if you have questions that are not answered in > the FAQ. > > We apologize that events beyond our control have caused us to change the > conference dates and for the inconvenience that this will cause you. We > nevertheless look forward to seeing you in Eilat for an exciting > conference in January 2007! > > Best regards, > Hershel Safer and Haim Wolfson > ECCB Conference Chairs > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board