From yvan.strahm at gmail.com Mon Nov 10 08:18:51 2008 From: yvan.strahm at gmail.com (Yvan Strahm) Date: Mon, 10 Nov 2008 14:18:51 +0100 Subject: [BiO BB] protein sequence for all organism Message-ID: Hello All, I want to get the all the possible protein sequence for eukaryote. I already downloaded nr from the NCBI ftp site, but i wish to have them sorted by organism, one folder per species. Currently I am downloading data from ftp://ftp.ncbi.nih.gov/genomes/X/protein/protein.fa.gz . Does this resource represent all the proteins sequences which are available in genbank? Or do you know a better way of getting a comprehensive data set? Thanks for your help and time, Cheers, yvan From marty.gollery at gmail.com Mon Nov 10 17:30:02 2008 From: marty.gollery at gmail.com (Martin Gollery) Date: Mon, 10 Nov 2008 14:30:02 -0800 Subject: [BiO BB] protein sequence for all organism In-Reply-To: References: Message-ID: Yvan, I believe this would give you a very large number of folders. You may have better luck with Uniprot, which will allow you to download data from taxonomic groups instead of individual species, reducing the number of folders to a half million or so. Check out the uniprot download options at: http://www.uniprot.org/taxonomy/ Cheers, Marty On Mon, Nov 10, 2008 at 5:18 AM, Yvan Strahm wrote: > Hello All, > > I want to get the all the possible protein sequence for eukaryote. > I already downloaded nr from the NCBI ftp site, but i wish to have them > sorted by organism, one folder per species. Currently I am downloading data > from ftp://ftp.ncbi.nih.gov/genomes/X/protein/protein.fa.gz . Does this > resource represent all the proteins sequences which are available in > genbank? Or do you know a better way of getting a comprehensive data set? > > Thanks for your help and time, > Cheers, > yvan > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist TimeLogic- a Division of Active Motif North America Toll Free (877) 222-9543 ext. 6 Direct (760) 431-1263 ext. 6 From Sterten at aol.com Tue Nov 11 00:32:16 2008 From: Sterten at aol.com (Sterten at aol.com) Date: Tue, 11 Nov 2008 00:32:16 EST Subject: [BiO BB] protein sequence for all organism Message-ID: checking: _ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt_ (ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt) is it about 400GB in total ? including description and nucleotide-sequences, so maybe ~100GB for protein sequences human,chicken, (what else) not included ? From veredcc at bgu.ac.il Tue Nov 11 06:48:46 2008 From: veredcc at bgu.ac.il (Vered Caspi) Date: Tue, 11 Nov 2008 13:48:46 +0200 Subject: [BiO BB] Analysis of mass spectrometry results using custom protein databases Message-ID: <008401c943f3$742167b0$5c643710$@ac.il> Hello, I received mass spec data for proteins (tryptic peptides) of a rare organism. Data analysis using web-based programs against standard protein databases did not yield results. We would like to run the analysis against a collection of the protein sequences from our organism, which we have constructed in-house. My question is whether there is a public program which can accept the protein sequences, "cut" them bioinformatically, and use that to identify the proteins analyzed in the mass sptrometry. Vered ______________________________________________________________ Vered Caspi, Ph.D. Bioinformatics Core Facility, Head National Institute for Biotechnology in the Negev Building 39, room 214 Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Email: veredcc at bgumail.bgu.ac.il Tel: 08-6479034 054-7915969 Fax: 08-6472983 http://bioinfo.bgu.ac.il ______________________________________________________________ From me at hongyu.org Tue Nov 11 15:50:42 2008 From: me at hongyu.org (Hongyu Zhang) Date: Tue, 11 Nov 2008 12:50:42 -0800 (PST) Subject: [BiO BB] protein sequence for all organism Message-ID: <761851.71833.qm@web51409.mail.re2.yahoo.com> My solution is to download the taxonomy files from Genebank, which contain the information of the taxonomy numbers for all GI numbers and the hierarchical taxonomy tree structure. You can write a program to partition the protein NR file into separated files/folders, each belonging to a specific taxonomy number that is a descendant of the eukaryote node in the taxonomy tree. The location of the Genbank taxonomy files is ftp://ftp.ncbi.nih.gov/pub/taxonomy/ From idoerg at gmail.com Wed Nov 12 18:07:21 2008 From: idoerg at gmail.com (Iddo Friedberg) Date: Wed, 12 Nov 2008 15:07:21 -0800 Subject: [BiO BB] Analysis of mass spectrometry results using custom protein databases In-Reply-To: <008401c943f3$742167b0$5c643710$@ac.il> References: <008401c943f3$742167b0$5c643710$@ac.il> Message-ID: Have you tried cutdb? http://cutdb.burnham.org/ On Tue, Nov 11, 2008 at 3:48 AM, Vered Caspi wrote: > Hello, > > I received mass spec data for proteins (tryptic peptides) of a rare > organism. Data analysis using web-based programs against standard protein > databases did not yield results. > > We would like to run the analysis against a collection of the protein > sequences from our organism, which we have constructed in-house. > > My question is whether there is a public program which can accept the > protein sequences, "cut" them bioinformatically, and use that to identify > the proteins analyzed in the mass sptrometry. > > Vered > > ______________________________________________________________ > Vered Caspi, Ph.D. > Bioinformatics Core Facility, Head > National Institute for Biotechnology in the Negev > Building 39, room 214 > Ben-Gurion University of the Negev > Beer-Sheva 84105, Israel > > Email: veredcc at bgumail.bgu.ac.il > Tel: 08-6479034 054-7915969 > Fax: 08-6472983 > > http://bioinfo.bgu.ac.il > ______________________________________________________________ > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Iddo Friedberg, Ph.D. Atkinson Hall, mail code 0446 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0446, USA T: +1 (858) 534-0570 http://iddo-friedberg.org From idoerg at gmail.com Wed Nov 12 18:26:37 2008 From: idoerg at gmail.com (Iddo Friedberg) Date: Wed, 12 Nov 2008 15:26:37 -0800 Subject: [BiO BB] Analysis of mass spectrometry results using custom protein databases In-Reply-To: <008401c943f3$742167b0$5c643710$@ac.il> References: <008401c943f3$742167b0$5c643710$@ac.il> Message-ID: Also, there is pops: http://pops.csse.monash.edu.au/ On Tue, Nov 11, 2008 at 3:48 AM, Vered Caspi wrote: > Hello, > > I received mass spec data for proteins (tryptic peptides) of a rare > organism. Data analysis using web-based programs against standard protein > databases did not yield results. > > We would like to run the analysis against a collection of the protein > sequences from our organism, which we have constructed in-house. > > My question is whether there is a public program which can accept the > protein sequences, "cut" them bioinformatically, and use that to identify > the proteins analyzed in the mass sptrometry. > > Vered > > ______________________________________________________________ > Vered Caspi, Ph.D. > Bioinformatics Core Facility, Head > National Institute for Biotechnology in the Negev > Building 39, room 214 > Ben-Gurion University of the Negev > Beer-Sheva 84105, Israel > > Email: veredcc at bgumail.bgu.ac.il > Tel: 08-6479034 054-7915969 > Fax: 08-6472983 > > http://bioinfo.bgu.ac.il > ______________________________________________________________ > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Iddo Friedberg, Ph.D. Atkinson Hall, mail code 0446 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0446, USA T: +1 (858) 534-0570 http://iddo-friedberg.org From marchywka at hotmail.com Wed Nov 12 19:38:07 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 12 Nov 2008 19:38:07 -0500 Subject: [BiO BB] Analysis of mass spectrometry results using custom protein databases In-Reply-To: <008401c943f3$742167b0$5c643710$@ac.il> References: <008401c943f3$742167b0$5c643710$@ac.il> Message-ID: More of a question than an answer but what exactly are you doing? Are these cleanly sliced or were they digested in an environment where they may have been further modified? For that matter, is the organism unusual enough to suspect unusual post-translational modifications? etc. > From: veredcc at bgu.ac.il > To: bbb at bioinformatics.org > Date: Tue, 11 Nov 2008 13:48:46 +0200 > Subject: [BiO BB] Analysis of mass spectrometry results using custom protein databases > > Hello, > > I received mass spec data for proteins (tryptic peptides) of a rare > organism. Data analysis using web-based programs against standard protein > databases did not yield results. > > We would like to run the analysis against a collection of the protein > sequences from our organism, which we have constructed in-house. > > My question is whether there is a public program which can accept the > protein sequences, "cut" them bioinformatically, and use that to identify > the proteins analyzed in the mass sptrometry. > > Vered > > ______________________________________________________________ > Vered Caspi, Ph.D. > Bioinformatics Core Facility, Head > National Institute for Biotechnology in the Negev > Building 39, room 214 > Ben-Gurion University of the Negev > Beer-Sheva 84105, Israel > > Email: veredcc at bgumail.bgu.ac.il > Tel: 08-6479034 054-7915969 > Fax: 08-6472983 > > http://bioinfo.bgu.ac.il > ______________________________________________________________ > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Get 5 GB of storage with Windows Live Hotmail. http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_5gb_112008 From abhishek.vit at gmail.com Wed Nov 12 17:55:41 2008 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Wed, 12 Nov 2008 14:55:41 -0800 Subject: [BiO BB] Analysis of mass spectrometry results using custom protein databases In-Reply-To: <008401c943f3$742167b0$5c643710$@ac.il> References: <008401c943f3$742167b0$5c643710$@ac.il> Message-ID: Dear Dr Vered It depends what kind of mass spec data (file formats) you have received. In order to analyze the proteins in the Mass Spec data there is a lengthy process which I will try to zip in couple of lines. Based on the data format you might have to pick up search engine. Search Engines (X!Tandem, Myrimatch are open source programs ) which can do this for you. The search results have to statistically validated in order to be certain that identifications by these search engines are correct coz many at times they are not. I work in the Proteomics Lab at Institute for Systems Biology, Aebersold Group. We have our own in house MS/MS analysis pipeline TPP ( http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP). This software is open source and includes X!Tandem bundled in. It would be a great place for your lab to start. In case you prefer we may gladly analyze the data for you and collaborate with you on this project. Let me know what you feel. Best Abhishek Pratap On Tue, Nov 11, 2008 at 3:48 AM, Vered Caspi wrote: > Hello, > > I received mass spec data for proteins (tryptic peptides) of a rare > organism. Data analysis using web-based programs against standard protein > databases did not yield results. > > We would like to run the analysis against a collection of the protein > sequences from our organism, which we have constructed in-house. > > My question is whether there is a public program which can accept the > protein sequences, "cut" them bioinformatically, and use that to identify > the proteins analyzed in the mass sptrometry. > > Vered > > ______________________________________________________________ > Vered Caspi, Ph.D. > Bioinformatics Core Facility, Head > National Institute for Biotechnology in the Negev > Building 39, room 214 > Ben-Gurion University of the Negev > Beer-Sheva 84105, Israel > > Email: veredcc at bgumail.bgu.ac.il > Tel: 08-6479034 054-7915969 > Fax: 08-6472983 > > http://bioinfo.bgu.ac.il > ______________________________________________________________ > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- ----------------------------- Abhishek Pratap Assistant, Aebersold Lab Institute for Systems Biology, Seattle 1441 N. 34th St. Seattle, WA 98103 ph 001-(206) 732-1419 fax 001-(206) 299-6572 www.systemsbiology.org Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From jforment at ibmcp.upv.es Wed Nov 12 19:00:54 2008 From: jforment at ibmcp.upv.es (Javier Forment Millet) Date: Thu, 13 Nov 2008 01:00:54 +0100 Subject: [BiO BB] PDB files on Cn3D Message-ID: <1226534454.491b6e36e7d14@webmail.upv.es> Hi, all... Does anyone know any way to open custom .pdb files with the Cn3D tool? -- Javier Forment Millet Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta E Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain Tlf.:+34-96-3877858 FAX: +34-96-3877859 jforment at ibmcp.upv.es From skhadar at gmail.com Fri Nov 14 07:17:04 2008 From: skhadar at gmail.com (Shameer Khadar) Date: Fri, 14 Nov 2008 17:47:04 +0530 Subject: [BiO BB] PDB files on Cn3D In-Reply-To: <1226534454.491b6e36e7d14@webmail.upv.es> References: <1226534454.491b6e36e7d14@webmail.upv.es> Message-ID: Hi, I trust you can download a standalone version of Cn3D from NCBI and use it for visualization of custom .pdb files. http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml On Thu, Nov 13, 2008 at 5:30 AM, Javier Forment Millet < jforment at ibmcp.upv.es> wrote: > Hi, all... Does anyone know any way to open custom .pdb files with the Cn3D > tool? > > -- > Javier Forment Millet > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta > E > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > Tlf.:+34-96-3877858 > FAX: +34-96-3877859 > jforment at ibmcp.upv.es > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- K. Shameer NCBS - TIFR ========================================= | Indulge | Innovate | Inspire | From marchywka at hotmail.com Mon Nov 17 11:17:43 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 17 Nov 2008 11:17:43 -0500 Subject: [BiO BB] PDB files on Cn3D In-Reply-To: References: <1226534454.491b6e36e7d14@webmail.upv.es> Message-ID: Have you actually tried this? I have an older version and I tried to open one and it didn't like it but I never followed up- could have been corrupt etc. I usually use chime, rasmol, or my own custom viewer for pdb files and only use Cn3D for some of the pubmed entries. > Date: Fri, 14 Nov 2008 17:47:04 +0530> From: skhadar at gmail.com> To: bbb at bioinformatics.org> Subject: Re: [BiO BB] PDB files on Cn3D> > Hi,> > I trust you can download a standalone version of Cn3D from NCBI and use it> for visualization of custom .pdb files.> http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml> > > On Thu, Nov 13, 2008 at 5:30 AM, Javier Forment Millet <> jforment at ibmcp.upv.es> wrote:> > > Hi, all... Does anyone know any way to open custom .pdb files with the Cn3D> > tool?> >> > --> > Javier Forment Millet> > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV> > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta> > E> > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain> > Tlf.:+34-96-3877858> > FAX: +34-96-3877859> > jforment at ibmcp.upv.es> >> >> > _______________________________________________> > BBB mailing list> > BBB at bioinformatics.org> > http://www.bioinformatics.org/mailman/listinfo/bbb> >> > > > -- > K. Shameer> NCBS - TIFR> > =========================================> | Indulge | Innovate | Inspire |> _______________________________________________> BBB mailing list> BBB at bioinformatics.org> http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Color coding for safety: Windows Live Hotmail alerts you to suspicious email. http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_safety_112008 From jforment at ibmcp.upv.es Mon Nov 17 13:24:22 2008 From: jforment at ibmcp.upv.es (Javier Forment Millet) Date: Mon, 17 Nov 2008 19:24:22 +0100 Subject: [BiO BB] PDB files on Cn3D In-Reply-To: References: <1226534454.491b6e36e7d14@webmail.upv.es> Message-ID: <1226946262.4921b6d6b14d5@webmail.upv.es> AFAIK, Cn3D is not able to open .pdb files. It uses a specific format. >From the Cn3D FAQ (http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dfaq.shtml#NOPDB): Cn3D reads only data files from the MMDB database, not PDB formatted records. MMDB is derived from the PDB database, but is corrected for naming-problems, performs domain-splitting, assigns consistent secondary structures, adds complete bonding information, and finally makes protein sequences corresponding exactly to the residues that appear in the structure. This work is done by a series of programs not possible to include in Cn3D. So... Quoting Shameer Khadar : > Hi, > > I trust you can download a standalone version of Cn3D from NCBI and use it > for visualization of custom .pdb files. > http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml > > > On Thu, Nov 13, 2008 at 5:30 AM, Javier Forment Millet < > jforment at ibmcp.upv.es> wrote: > > > Hi, all... Does anyone know any way to open custom .pdb files with the Cn3D > > tool? > > > > -- > > Javier Forment Millet > > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta > > E > > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > > Tlf.:+34-96-3877858 > > FAX: +34-96-3877859 > > jforment at ibmcp.upv.es > > > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > K. Shameer > NCBS - TIFR > > ========================================= > | Indulge | Innovate | Inspire | > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Javier Forment Millet Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta E Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain Tlf.:+34-96-3877858 FAX: +34-96-3877859 jforment at ibmcp.upv.es From skhadar at gmail.com Mon Nov 17 22:26:44 2008 From: skhadar at gmail.com (Shameer Khadar) Date: Tue, 18 Nov 2008 08:56:44 +0530 Subject: [BiO BB] PDB files on Cn3D In-Reply-To: <1226946262.4921b6d6b14d5@webmail.upv.es> References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> Message-ID: Is this MMDB format avaialable through openbabel for format conversion ? On Mon, Nov 17, 2008 at 11:54 PM, Javier Forment Millet < jforment at ibmcp.upv.es> wrote: > AFAIK, Cn3D is not able to open .pdb files. It uses a specific format. > > >From the Cn3D FAQ > (http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dfaq.shtml#NOPDB): > > Cn3D reads only data files from the MMDB database, not PDB formatted > records. > MMDB is derived from the PDB database, but is corrected for > naming-problems, > performs domain-splitting, assigns consistent secondary structures, adds > complete bonding information, and finally makes protein sequences > corresponding > exactly to the residues that appear in the structure. This work is done by > a > series of programs not possible to include in Cn3D. > > So... > > > > > Quoting Shameer Khadar : > > > Hi, > > > > I trust you can download a standalone version of Cn3D from NCBI and use > it > > for visualization of custom .pdb files. > > http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml > > > > > > On Thu, Nov 13, 2008 at 5:30 AM, Javier Forment Millet < > > jforment at ibmcp.upv.es> wrote: > > > > > Hi, all... Does anyone know any way to open custom .pdb files with the > Cn3D > > > tool? > > > > > > -- > > > Javier Forment Millet > > > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > > > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 > Puerta > > > E > > > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > > > Tlf.:+34-96-3877858 > > > FAX: +34-96-3877859 > > > jforment at ibmcp.upv.es > > > > > > > > > _______________________________________________ > > > BBB mailing list > > > BBB at bioinformatics.org > > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > > > > -- > > K. Shameer > > NCBS - TIFR > > > > ========================================= > > | Indulge | Innovate | Inspire | > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > -- > Javier Forment Millet > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta > E > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > Tlf.:+34-96-3877858 > FAX: +34-96-3877859 > jforment at ibmcp.upv.es > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > -- K. Shameer ------------------------------------------------------------ Computational Biology Lab, NCBS - TIFR Molecular Biophysics Unit, IISc From yvan.strahm at gmail.com Tue Nov 18 04:17:41 2008 From: yvan.strahm at gmail.com (Yvan Strahm) Date: Tue, 18 Nov 2008 10:17:41 +0100 Subject: [BiO BB] protein sequence for all organism In-Reply-To: <761851.71833.qm@web51409.mail.re2.yahoo.com> References: <761851.71833.qm@web51409.mail.re2.yahoo.com> Message-ID: Thanks every one for the tips. I ended up using the taxonomy files from genbank and uniprot and sorting them according to the organism. Cheers, yvan On Tue, Nov 11, 2008 at 9:50 PM, Hongyu Zhang wrote: > My solution is to download the taxonomy files from Genebank, which contain > the information of the taxonomy numbers for all GI numbers and the > hierarchical taxonomy tree structure. You can write a program to partition > the protein NR file into separated files/folders, each belonging to a > specific taxonomy number that is a descendant of the eukaryote node in the > taxonomy tree. > > The location of the Genbank taxonomy files is > ftp://ftp.ncbi.nih.gov/pub/taxonomy/ > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From kailsen at yahoo.com Tue Nov 18 08:47:22 2008 From: kailsen at yahoo.com (senthil kumar) Date: Tue, 18 Nov 2008 19:17:22 +0530 (IST) Subject: [BiO BB] how to grep DNA from protein References: <1226534454.491b6e36e7d14@webmail.upv.es> Message-ID: <149708.18845.qm@web94814.mail.in2.yahoo.com> Hi friends, i have a serious problem, I wanted to grep all the nucleic acid Coordiantes line from a ribosome PDBfile and store in separate file, so i wish to do for some twenty files.. any help is welcomed, think its is possible by perl or awk or sed .or "shell Grep " ??? Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ From nir at rosettadesigngroup.com Tue Nov 18 09:33:18 2008 From: nir at rosettadesigngroup.com (Nir London) Date: Tue, 18 Nov 2008 16:33:18 +0200 Subject: [BiO BB] The Macromolecular Modeling Blog Message-ID: <9A3F9914-0C4F-4E4F-AFC6-F186481B30ED@rosettadesigngroup.com> Hi all, and a special hi to the structural biology fans :) We started a new blog on all that is related to Macromolecular Modeling http://rosettadesigngroup.com/blog/ We opened this blog in order to provide the modeling community with a helpful resource. Keep updated with what's new in the modeling world, read executive summaries of the latest literature and stay in touch with pears. please check it out and tell me what you think... If any of you is interested in writing for the blog I'd be very happy if you contact me. Cheers, Nir London. Rosetta Design Group http://rosettadesigngroup.com/ From abhishek.vit at gmail.com Tue Nov 18 13:26:51 2008 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 18 Nov 2008 10:26:51 -0800 Subject: [BiO BB] how to grep DNA from protein In-Reply-To: <149708.18845.qm@web94814.mail.in2.yahoo.com> References: <1226534454.491b6e36e7d14@webmail.upv.es> <149708.18845.qm@web94814.mail.in2.yahoo.com> Message-ID: Dear Senthil You have mentioned all the right alternatives. If you could past a line from this file format and what pattern you would like to catch. I might be able to propose a regex for the same. Thanks, -Abhishek On Tue, Nov 18, 2008 at 5:47 AM, senthil kumar wrote: > > > Hi friends, > i have a serious problem, I wanted to grep all the nucleic acid > Coordiantes line from a ribosome PDBfile and store in separate file, so i > wish to do for some twenty files.. any help is welcomed, > think its is possible by perl or awk or sed .or "shell Grep " ??? > > > > Add more friends to your messenger and enjoy! Go to > http://messenger.yahoo.com/invite/ > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- ----------------------------- Abhishek Pratap Assistant, Aebersold Lab Institute for Systems Biology, Seattle 1441 N. 34th St. Seattle, WA 98103 ph 001-(206) 732-1419 fax 001-(206) 299-6572 www.systemsbiology.org Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From jforment at ibmcp.upv.es Wed Nov 19 05:04:48 2008 From: jforment at ibmcp.upv.es (Javier Forment Millet) Date: Wed, 19 Nov 2008 11:04:48 +0100 Subject: [BiO BB] PDB files on Cn3D In-Reply-To: References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> Message-ID: <1227089088.4923e4c01fbc6@webmail.upv.es> It seems that MMDB format is not available through openbabel: see all the formats available through openbabel at: http://openbabel.org/wiki/Category:Formats Quoting Shameer Khadar : > Is this MMDB format avaialable through openbabel for format conversion ? > > On Mon, Nov 17, 2008 at 11:54 PM, Javier Forment Millet < > jforment at ibmcp.upv.es> wrote: > > > AFAIK, Cn3D is not able to open .pdb files. It uses a specific format. > > > > >From the Cn3D FAQ > > (http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dfaq.shtml#NOPDB): > > > > Cn3D reads only data files from the MMDB database, not PDB formatted > > records. > > MMDB is derived from the PDB database, but is corrected for > > naming-problems, > > performs domain-splitting, assigns consistent secondary structures, adds > > complete bonding information, and finally makes protein sequences > > corresponding > > exactly to the residues that appear in the structure. This work is done by > > a > > series of programs not possible to include in Cn3D. > > > > So... > > > > > > > > > > Quoting Shameer Khadar : > > > > > Hi, > > > > > > I trust you can download a standalone version of Cn3D from NCBI and use > > it > > > for visualization of custom .pdb files. > > > http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml > > > > > > > > > On Thu, Nov 13, 2008 at 5:30 AM, Javier Forment Millet < > > > jforment at ibmcp.upv.es> wrote: > > > > > > > Hi, all... Does anyone know any way to open custom .pdb files with the > > Cn3D > > > > tool? > > > > > > > > -- > > > > Javier Forment Millet > > > > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > > > > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 > > Puerta > > > > E > > > > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > > > > Tlf.:+34-96-3877858 > > > > FAX: +34-96-3877859 > > > > jforment at ibmcp.upv.es > > > > > > > > > > > > _______________________________________________ > > > > BBB mailing list > > > > BBB at bioinformatics.org > > > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > > > > > > > > > -- > > > K. Shameer > > > NCBS - TIFR > > > > > > ========================================= > > > | Indulge | Innovate | Inspire | > > > _______________________________________________ > > > BBB mailing list > > > BBB at bioinformatics.org > > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > > -- > > Javier Forment Millet > > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta > > E > > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > > Tlf.:+34-96-3877858 > > FAX: +34-96-3877859 > > jforment at ibmcp.upv.es > > > > > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > -- > K. Shameer > ------------------------------------------------------------ > Computational Biology Lab, NCBS - TIFR > Molecular Biophysics Unit, IISc > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Javier Forment Millet Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta E Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain Tlf.:+34-96-3877858 FAX: +34-96-3877859 jforment at ibmcp.upv.es From skhadar at gmail.com Wed Nov 19 09:09:04 2008 From: skhadar at gmail.com (Shameer Khadar) Date: Wed, 19 Nov 2008 19:39:04 +0530 Subject: [BiO BB] PDB files on Cn3D In-Reply-To: <1226946262.4921b6d6b14d5@webmail.upv.es> References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> Message-ID: http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtutP2.shtml#PDB_data This link says Structures in PDB can be visualised using Cn3D. On Mon, Nov 17, 2008 at 11:54 PM, Javier Forment Millet < jforment at ibmcp.upv.es> wrote: > AFAIK, Cn3D is not able to open .pdb files. It uses a specific format. > > >From the Cn3D FAQ > (http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dfaq.shtml#NOPDB): > > Cn3D reads only data files from the MMDB database, not PDB formatted > records. > MMDB is derived from the PDB database, but is corrected for > naming-problems, > performs domain-splitting, assigns consistent secondary structures, adds > complete bonding information, and finally makes protein sequences > corresponding > exactly to the residues that appear in the structure. This work is done by > a > series of programs not possible to include in Cn3D. > > So... > > > > > Quoting Shameer Khadar : > > > Hi, > > > > I trust you can download a standalone version of Cn3D from NCBI and use > it > > for visualization of custom .pdb files. > > http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml > > > > > > On Thu, Nov 13, 2008 at 5:30 AM, Javier Forment Millet < > > jforment at ibmcp.upv.es> wrote: > > > > > Hi, all... Does anyone know any way to open custom .pdb files with the > Cn3D > > > tool? > > > > > > -- > > > Javier Forment Millet > > > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > > > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 > Puerta > > > E > > > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > > > Tlf.:+34-96-3877858 > > > FAX: +34-96-3877859 > > > jforment at ibmcp.upv.es > > > > > > > > > _______________________________________________ > > > BBB mailing list > > > BBB at bioinformatics.org > > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > > > > -- > > K. Shameer > > NCBS - TIFR > > > > ========================================= > > | Indulge | Innovate | Inspire | > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > -- > Javier Forment Millet > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta > E > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > Tlf.:+34-96-3877858 > FAX: +34-96-3877859 > jforment at ibmcp.upv.es > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > -- K. Shameer ------------------------------------------------------------ Computational Biology Lab, NCBS - TIFR Molecular Biophysics Unit, IISc From jforment at ibmcp.upv.es Wed Nov 19 13:19:44 2008 From: jforment at ibmcp.upv.es (Javier Forment Millet) Date: Wed, 19 Nov 2008 19:19:44 +0100 Subject: [BiO BB] PDB files on Cn3D In-Reply-To: References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> Message-ID: <1227118784.492458c03ec5a@webmail.upv.es> Yes, but I understand that it does not use directly the .pdb file from PDB. It uses a MMDB-formatted file from MMDB. Maybe I'm wrong, but I understand from this link that Cn3D just uses the PDB ID to identify the MMDB record corresponding to that structure. Quoting Shameer Khadar : > http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtutP2.shtml#PDB_data > This link says Structures in PDB can be visualised using Cn3D. > > > On Mon, Nov 17, 2008 at 11:54 PM, Javier Forment Millet < > jforment at ibmcp.upv.es> wrote: > > > AFAIK, Cn3D is not able to open .pdb files. It uses a specific format. > > > > >From the Cn3D FAQ > > (http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dfaq.shtml#NOPDB): > > > > Cn3D reads only data files from the MMDB database, not PDB formatted > > records. > > MMDB is derived from the PDB database, but is corrected for > > naming-problems, > > performs domain-splitting, assigns consistent secondary structures, adds > > complete bonding information, and finally makes protein sequences > > corresponding > > exactly to the residues that appear in the structure. This work is done by > > a > > series of programs not possible to include in Cn3D. > > > > So... > > > > > > > > > > Quoting Shameer Khadar : > > > > > Hi, > > > > > > I trust you can download a standalone version of Cn3D from NCBI and use > > it > > > for visualization of custom .pdb files. > > > http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml > > > > > > > > > On Thu, Nov 13, 2008 at 5:30 AM, Javier Forment Millet < > > > jforment at ibmcp.upv.es> wrote: > > > > > > > Hi, all... Does anyone know any way to open custom .pdb files with the > > Cn3D > > > > tool? > > > > > > > > -- > > > > Javier Forment Millet > > > > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > > > > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 > > Puerta > > > > E > > > > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > > > > Tlf.:+34-96-3877858 > > > > FAX: +34-96-3877859 > > > > jforment at ibmcp.upv.es > > > > > > > > > > > > _______________________________________________ > > > > BBB mailing list > > > > BBB at bioinformatics.org > > > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > > > > > > > > > -- > > > K. Shameer > > > NCBS - TIFR > > > > > > ========================================= > > > | Indulge | Innovate | Inspire | > > > _______________________________________________ > > > BBB mailing list > > > BBB at bioinformatics.org > > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > > -- > > Javier Forment Millet > > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta > > E > > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > > Tlf.:+34-96-3877858 > > FAX: +34-96-3877859 > > jforment at ibmcp.upv.es > > > > > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > -- > K. Shameer > ------------------------------------------------------------ > Computational Biology Lab, NCBS - TIFR > Molecular Biophysics Unit, IISc > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Javier Forment Millet Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta E Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain Tlf.:+34-96-3877858 FAX: +34-96-3877859 jforment at ibmcp.upv.es From xiaowei.jiang at msn.com Fri Nov 21 10:14:04 2008 From: xiaowei.jiang at msn.com (Xiaowei Jiang) Date: Fri, 21 Nov 2008 15:14:04 +0000 Subject: [BiO BB] Save protein structure image as an adobe SVG format file In-Reply-To: <1227118784.492458c03ec5a@webmail.upv.es> References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> <1227118784.492458c03ec5a@webmail.upv.es> Message-ID: Hi fellows, Does anyone know a PDB viewer software or a way, in which I can save image directly as an adobe SVG format file? Thanks in advance!! Cheers, Xiaowei From pandey.gaurav at gmail.com Mon Nov 24 13:31:29 2008 From: pandey.gaurav at gmail.com (Gaurav Pandey) Date: Mon, 24 Nov 2008 12:31:29 -0600 Subject: [BiO BB] RefSeq ids to gene names Message-ID: <627ca1900811241031l162088a9mca5c5c7e9f06a@mail.gmail.com> Hello, Where can I get a text/excel file with a mapping of RefSeq id's to their common gene names (such as SYN2, SERPINA3 etc), particularly for homo sapiens? The NCBI ftp site was not extremely useful. Also, some of the RefSeq IDs I have are of the form 'Contig30743_RC'. Are these also RefSeq IDs? Any help will be deeply appreciated. Thanks! Gaurav -- Gaurav Pandey Email: gaurav at cs.umn.edu Computer Science Department Webpage: www.cs.umn.edu/~gaurav University of Minnesota Tel: 612-701-2494 From dankoc at gmail.com Mon Nov 24 17:18:48 2008 From: dankoc at gmail.com (Charles Danko) Date: Mon, 24 Nov 2008 17:18:48 -0500 Subject: [BiO BB] RefSeq ids to gene names In-Reply-To: <627ca1900811241031l162088a9mca5c5c7e9f06a@mail.gmail.com> References: <627ca1900811241031l162088a9mca5c5c7e9f06a@mail.gmail.com> Message-ID: <8adccabf0811241418xba80d54i831ed92f9a5b7689@mail.gmail.com> Hi, Gaurav, I don't think that those are RefSeq IDs. In general, the easiest way to do something like this is using biomart: http://www.biomart.org/. 1. Go to martview. 2. Select the database and species. 3. Do NOT change the selection under filters. 5. Under attributes, select any ID type that you want. The result will be a table of ID associations that you can export in the format of your choice... Good luck! Charles On Mon, Nov 24, 2008 at 1:31 PM, Gaurav Pandey wrote: > Hello, > > Where can I get a text/excel file with a mapping of RefSeq id's to their > common gene names (such as SYN2, SERPINA3 etc), particularly for homo > sapiens? The NCBI ftp site was not extremely useful. > > Also, some of the RefSeq IDs I have are of the form 'Contig30743_RC'. Are > these also RefSeq IDs? > > Any help will be deeply appreciated. Thanks! > > Gaurav > > -- > Gaurav Pandey Email: gaurav at cs.umn.edu > Computer Science Department Webpage: www.cs.umn.edu/~gaurav > University of Minnesota Tel: 612-701-2494 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From marchywka at hotmail.com Mon Nov 24 18:14:46 2008 From: marchywka at hotmail.com (Mike Marchywka ) Date: Mon, 24 Nov 2008 23:14:46 +0000 Subject: [BiO BB] RefSeq ids to gene names Message-ID: Generally for things like this, it can be easier to download a flat text file of the db contents and use grep to get what you want. I used to do this with eutilz results and now use for other db sources. Does the source file exist as a zip on their ftp site? Just download that and use Cygwin grep and sed. ------Original Message------ From: Charles Danko To: bbb at bioinformatics.org Sent: Nov 24, 2008 5:18 PM Subject: Re: [BiO BB] RefSeq ids to gene names Hi, Gaurav, I don't think that those are RefSeq IDs. In general, the easiest way to do something like this is using biomart: http://www.biomart.org/ . 1. Go to martview. 2. Select the database and species. 3. Do NOT change the selection under filters. 5. Under attributes, select any ID type that you want. The result will be a table of ID associations that you can export in the format of your choice... Good luck! Charles On Mon, Nov 24, 2008 at 1:31 PM, Gaurav Pandey wrote: > Hello, > > Where can I get a text/excel file with a mapping of RefSeq id's to their > common gene names (such as SYN2, SERPINA3 etc), particularly for homo > sapiens? The NCBI ftp site was not extremely useful. > > Also, some of the RefSeq IDs I? have are of the form 'Contig30743_RC'. Are > these also RefSeq IDs? > > Any help will be deeply appreciated. Thanks! > > Gaurav > > -- > Gaurav Pandey????????????????????????????????? Email: gaurav at cs.umn.edu > Computer Science Department????? Webpage: www.cs.umn.edu/~gaurav > University of Minnesota??????????????????? Tel: 612-701-2494 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb Sent from my Verizon Wireless BlackBerry From shreyasee.pradhan at gmail.com Mon Nov 24 18:36:35 2008 From: shreyasee.pradhan at gmail.com (Shreyasee) Date: Tue, 25 Nov 2008 07:36:35 +0800 Subject: [BiO BB] Save protein structure image as an adobe SVG format file In-Reply-To: References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> <1227118784.492458c03ec5a@webmail.upv.es> Message-ID: Hi, For viewing PDB files you can use Swiss PDB viewer software. Its free !!! On Fri, Nov 21, 2008 at 11:14 PM, Xiaowei Jiang wrote: > Hi fellows, > > Does anyone know a PDB viewer software or a way, in which I can save image > directly as an adobe SVG format file? > > Thanks in advance!! > > Cheers, > Xiaowei > > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Thanks, Shreyasee From marchywka at hotmail.com Mon Nov 24 19:23:30 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 24 Nov 2008 19:23:30 -0500 Subject: [BiO BB] Save protein structure image as an adobe SVG format file In-Reply-To: References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> <1227118784.492458c03ec5a@webmail.upv.es> Message-ID: I guess the real question is, " what are you trying to do?" You could probably write a perl script to do this. The pdb is ascii, you just need to project 3D onto 2D and get some atom colors and radii. SVG AFAIK is all ascii XML which is easy to generate from a script. If you take all the atoms, project, sort on Z ( distance from viewer), and generat XML that would probably give you what you need. http://www.w3.org/Graphics/SVG/ the code to draw circles is pretty simple, http://www.w3.org/TR/SVG11/shapes.html> Date: Tue, 25 Nov 2008 07:36:35 +0800> From: shreyasee.pradhan at gmail.com> To: bbb at bioinformatics.org> Subject: Re: [BiO BB] Save protein structure image as an adobe SVG format file> > Hi,> > For viewing PDB files you can use Swiss PDB viewer software. Its free !!!> > > On Fri, Nov 21, 2008 at 11:14 PM, Xiaowei Jiang wrote:> > > Hi fellows,> >> > Does anyone know a PDB viewer software or a way, in which I can save image> > directly as an adobe SVG format file?> >> > Thanks in advance!!> >> > Cheers,> > Xiaowei> >> >> >> >> > _______________________________________________> > BBB mailing list> > BBB at bioinformatics.org> > http://www.bioinformatics.org/mailman/listinfo/bbb> >> > > > -- > Thanks,> Shreyasee> _______________________________________________> BBB mailing list> BBB at bioinformatics.org> http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Proud to be a PC? Show the world. Download the ?I?m a PC? Messenger themepack now. hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ From boris.steipe at utoronto.ca Mon Nov 24 21:15:03 2008 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Mon, 24 Nov 2008 21:15:03 -0500 Subject: [BiO BB] Save protein structure image as an adobe SVG format file In-Reply-To: References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> <1227118784.492458c03ec5a@webmail.upv.es> Message-ID: <3E951E84-BE5A-42AC-A31F-BB16E240D52F@utoronto.ca> Meh. Simple Z-sorting is not intersecting spheres. If it's any non-trivial vector graphic representation you are trying to do, you might consider the following workflow: 3D-viewer -> View Matrix -> Molscript -> PS -> ps2svg B. On 24-Nov-08, at 7:23 PM, Mike Marchywka wrote: > > I guess the real question is, " what are you trying to do?" You could > probably write a perl script to do this. The pdb is ascii, you just > need to project > 3D onto 2D and get some atom colors and radii. SVG AFAIK is all ascii > XML which is easy to generate from a script. > If you take all the atoms, project, sort on Z ( distance from viewer), > and generat XML that would probably give you what you need. > http://www.w3.org/Graphics/SVG/ > > the code to draw circles is pretty simple, > http://www.w3.org/TR/SVG11/shapes.html> Date: Tue, 25 Nov 2008 > 07:36:35 +0800> From: shreyasee.pradhan at gmail.com> To: > bbb at bioinformatics.org> Subject: Re: [BiO BB] Save protein > structure image as an adobe SVG format file> > Hi,> > For viewing > PDB files you can use Swiss PDB viewer software. Its free !!!> > > > On Fri, Nov 21, 2008 at 11:14 PM, Xiaowei Jiang > wrote:> > > Hi fellows,> >> > Does anyone > know a PDB viewer software or a way, in which I can save image> > > directly as an adobe SVG format file?> >> > Thanks in advance!!> >> > > Cheers,> > Xiaowei> >> >> >> >> > > _______________________________________________> > BBB mailing > list> > BBB at bioinformatics.org> > http://www.bioinformatics.org/ > mailman/listinfo/bbb> >> > > > -- > Thanks,> Shreyasee> > _______________________________________________> BBB mailing list> > BBB at bioinformatics.org> http://www.bioinformatics.org/mailman/ > listinfo/bbb > _________________________________________________________________ > Proud to be a PC? Show the world. Download the ?I?m a PC? Messenger > themepack now. > hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From marchywka at hotmail.com Tue Nov 25 09:17:21 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 25 Nov 2008 09:17:21 -0500 Subject: [BiO BB] Save protein structure image as an adobe SVG format file In-Reply-To: <3E951E84-BE5A-42AC-A31F-BB16E240D52F@utoronto.ca> References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> <1227118784.492458c03ec5a@webmail.upv.es> <3E951E84-BE5A-42AC-A31F-BB16E240D52F@utoronto.ca> Message-ID: > From: boris.steipe at utoronto.ca > Date: Mon, 24 Nov 2008 21:15:03 -0500 > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] Save protein structure image as an adobe SVG format file > > Meh. > Simple Z-sorting is not intersecting spheres. > If it's any non-trivial vector graphic representation you are trying > to do, you might consider the following workflow: > 3D-viewer -> View Matrix -> Molscript -> PS -> ps2svg there is something called bkchem, http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/Structure_drawing and if you look at discussions the viewers don't obviously have svg output options. Certainly if you can't find direct svg output, conversion from another model-preserving output format would be great. But, I wouldn't dismiss the script approach immediately depending on your ultimate goals. A scriptable viewer could generate many views but you could also write a script without the viewer. Spheres aren't that hard for z-sorting, http://en.wikipedia.org/wiki/Bounding_volume > > > B. > > > > > On 24-Nov-08, at 7:23 PM, Mike Marchywka wrote: > >> >> I guess the real question is, " what are you trying to do?" You could >> probably write a perl script to do this. The pdb is ascii, you just >> need to project >> 3D onto 2D and get some atom colors and radii. SVG AFAIK is all ascii >> XML which is easy to generate from a script. >> If you take all the atoms, project, sort on Z ( distance from viewer), >> and generat XML that would probably give you what you need. >> http://www.w3.org/Graphics/SVG/ >> >> the code to draw circles is pretty simple, >> http://www.w3.org/TR/SVG11/shapes.html> Date: Tue, 25 Nov 2008 >> 07:36:35 +0800> From: shreyasee.pradhan at gmail.com> To: >> bbb at bioinformatics.org> Subject: Re: [BiO BB] Save protein >> structure image as an adobe SVG format file>> Hi,>> For viewing >> PDB files you can use Swiss PDB viewer software. Its free !!!>>> >> On Fri, Nov 21, 2008 at 11:14 PM, Xiaowei Jiang >> wrote:>>> Hi fellows,>>>> Does anyone >> know a PDB viewer software or a way, in which I can save image>> >> directly as an adobe SVG format file?>>>> Thanks in advance!!>>> >>> Cheers,>> Xiaowei>>>>>>>>>> >> _______________________________________________>> BBB mailing >> list>> BBB at bioinformatics.org>> http://www.bioinformatics.org/ >> mailman/listinfo/bbb>>>>>> --> Thanks,> Shreyasee> >> _______________________________________________> BBB mailing list> >> BBB at bioinformatics.org> http://www.bioinformatics.org/mailman/ >> listinfo/bbb >> _________________________________________________________________ >> Proud to be a PC? Show the world. Download the ?I?m a PC? Messenger >> themepack now. >> hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Get more done, have more fun, and stay more connected with Windows Mobile?. http://clk.atdmt.com/MRT/go/119642556/direct/01/ From marchywka at hotmail.com Fri Nov 28 08:15:27 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Fri, 28 Nov 2008 08:15:27 -0500 Subject: [BiO BB] informatics opportunity: "Human genomes in minutes?" Message-ID: This is a rather obvious thing to try, http://www.nature.com/news/2008/081120/full/news.2008.1245.html Erika Check Hayden A much-watched Silicon Valley company has published a proof of concept for its DNA-sequencing technology, which it hopes will one day be going through entire human genomes in minutes. Pacific Biosciences of Menlo Park, California, reports today that it can generate continuous stretches of DNA sequence up to thousands of base pairs long. But it may be something to watch for non-obvious bio-informatics opps. Is anyone aware of particularly interesting efforts related to the above? Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 415-264-8477 (w)<- use this 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: hotmail is getting cumbersom, try also marchywka at yahoo.com _________________________________________________________________ Access your email online and on the go with Windows Live Hotmail. http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_access_112008 From xiaowei.jiang at msn.com Tue Nov 25 09:05:37 2008 From: xiaowei.jiang at msn.com (Xiaowei Jiang) Date: Tue, 25 Nov 2008 14:05:37 +0000 Subject: [BiO BB] Save protein structure image as an adobe SVG format file In-Reply-To: <3E951E84-BE5A-42AC-A31F-BB16E240D52F@utoronto.ca> References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> <1227118784.492458c03ec5a@webmail.upv.es> <3E951E84-BE5A-42AC-A31F-BB16E240D52F@utoronto.ca> Message-ID: Hi guys, My point is : I just want to save whatever image I produce in a pdb viewer as a SVG image. So that I can use my Adobe Illustrator. It will save me some time if there is such viewer can provide such function. Cheers, Xiaowei -----Original Message----- From: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org] On Behalf Of Boris Steipe Sent: 25 November 2008 02:15 To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Save protein structure image as an adobe SVG format file Meh. Simple Z-sorting is not intersecting spheres. If it's any non-trivial vector graphic representation you are trying to do, you might consider the following workflow: 3D-viewer -> View Matrix -> Molscript -> PS -> ps2svg B. On 24-Nov-08, at 7:23 PM, Mike Marchywka wrote: > > I guess the real question is, " what are you trying to do?" You could > probably write a perl script to do this. The pdb is ascii, you just > need to project > 3D onto 2D and get some atom colors and radii. SVG AFAIK is all ascii > XML which is easy to generate from a script. > If you take all the atoms, project, sort on Z ( distance from viewer), > and generat XML that would probably give you what you need. > http://www.w3.org/Graphics/SVG/ > > the code to draw circles is pretty simple, > http://www.w3.org/TR/SVG11/shapes.html> Date: Tue, 25 Nov 2008 > 07:36:35 +0800> From: shreyasee.pradhan at gmail.com> To: > bbb at bioinformatics.org> Subject: Re: [BiO BB] Save protein > structure image as an adobe SVG format file> > Hi,> > For viewing > PDB files you can use Swiss PDB viewer software. Its free !!!> > > > On Fri, Nov 21, 2008 at 11:14 PM, Xiaowei Jiang > wrote:> > > Hi fellows,> >> > Does anyone > know a PDB viewer software or a way, in which I can save image> > > directly as an adobe SVG format file?> >> > Thanks in advance!!> >> > > Cheers,> > Xiaowei> >> >> >> >> > > _______________________________________________> > BBB mailing > list> > BBB at bioinformatics.org> > http://www.bioinformatics.org/ > mailman/listinfo/bbb> >> > > > -- > Thanks,> Shreyasee> > _______________________________________________> BBB mailing list> > BBB at bioinformatics.org> http://www.bioinformatics.org/mailman/ > listinfo/bbb > _________________________________________________________________ > Proud to be a PC? Show the world. Download the "I'm a PC" Messenger > themepack now. > hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From lijo.skb at gmail.com Tue Nov 25 11:00:33 2008 From: lijo.skb at gmail.com (Lijo) Date: Tue, 25 Nov 2008 21:30:33 +0530 Subject: [BiO BB] Save protein structure image as an adobe SVG format file In-Reply-To: References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> <1227118784.492458c03ec5a@webmail.upv.es> <3E951E84-BE5A-42AC-A31F-BB16E240D52F@utoronto.ca> Message-ID: have you tried with VMD? lijo On Tue, Nov 25, 2008 at 7:47 PM, Mike Marchywka wrote: > > > > > > > > From: boris.steipe at utoronto.ca > > Date: Mon, 24 Nov 2008 21:15:03 -0500 > > To: bbb at bioinformatics.org > > Subject: Re: [BiO BB] Save protein structure image as an adobe SVG format > file > > > > Meh. > > Simple Z-sorting is not intersecting spheres. > > If it's any non-trivial vector graphic representation you are trying > > to do, you might consider the following workflow: > > 3D-viewer -> View Matrix -> Molscript -> PS -> ps2svg > > there is something called bkchem, > > > http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/Structure_drawing > > and if you look at discussions the viewers don't obviously have svg output > options. > > Certainly if you can't find direct svg output, conversion from another > model-preserving > output format would be great. But, I wouldn't dismiss the script approach > immediately > depending on your ultimate goals. A scriptable viewer could generate many > views but you > could also write a script without the viewer. > > Spheres aren't that hard for z-sorting, > > > http://en.wikipedia.org/wiki/Bounding_volume > > > > > > > > > > > > > > > B. > > > > > > > > > > On 24-Nov-08, at 7:23 PM, Mike Marchywka wrote: > > > >> > >> I guess the real question is, " what are you trying to do?" You could > >> probably write a perl script to do this. The pdb is ascii, you just > >> need to project > >> 3D onto 2D and get some atom colors and radii. SVG AFAIK is all ascii > >> XML which is easy to generate from a script. > >> If you take all the atoms, project, sort on Z ( distance from viewer), > >> and generat XML that would probably give you what you need. > >> http://www.w3.org/Graphics/SVG/ > >> > >> the code to draw circles is pretty simple, > >> http://www.w3.org/TR/SVG11/shapes.html> Date: Tue, 25 Nov 2008 > >> 07:36:35 +0800> From: shreyasee.pradhan at gmail.com> To: > >> bbb at bioinformatics.org> Subject: Re: [BiO BB] Save protein > >> structure image as an adobe SVG format file>> Hi,>> For viewing > >> PDB files you can use Swiss PDB viewer software. Its free !!!>>> > >> On Fri, Nov 21, 2008 at 11:14 PM, Xiaowei Jiang > >> wrote:>>> Hi fellows,>>>> Does anyone > >> know a PDB viewer software or a way, in which I can save image>> > >> directly as an adobe SVG format file?>>>> Thanks in advance!!>>> > >>> Cheers,>> Xiaowei>>>>>>>>>> > >> _______________________________________________>> BBB mailing > >> list>> BBB at bioinformatics.org>> http://www.bioinformatics.org/ > >> mailman/listinfo/bbb>>>>>> --> Thanks,> Shreyasee> > >> _______________________________________________> BBB mailing list> > >> BBB at bioinformatics.org> http://www.bioinformatics.org/mailman/ > >> listinfo/bbb > >> _________________________________________________________________ > >> Proud to be a PC? Show the world. Download the "I'm a PC" Messenger > >> themepack now. > >> hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ > >> _______________________________________________ > >> BBB mailing list > >> BBB at bioinformatics.org > >> http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > _________________________________________________________________ > Get more done, have more fun, and stay more connected with Windows Mobile(R). > http://clk.atdmt.com/MRT/go/119642556/direct/01/ > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Centre for Bioinformatics, University of Kerala, India. +91 9446515705(res) From masulli at disi.unige.it Wed Nov 26 04:15:54 2008 From: masulli at disi.unige.it (Francesco Masulli) Date: Wed, 26 Nov 2008 10:15:54 +0100 Subject: [BiO BB] Call for Papers - IJCNN 2009 - Special Session on Soft Computing tools for Bioinformatics (Dec 15 2008 deadline) Message-ID: <200811261015.54920.masulli@disi.unige.it> [apologies for multiple posts] ----------------------------------------------------------------------------------------------------------------- CALL FOR PAPERS - Special Session on Soft Computing tools for Bioinformatics at International Joint Conference on Neural Networks (IJCNN 2009) sponsored by SIG on Bioinformatics of the International Neural Network Society (INNS) Location: Westin PeachTree Hotel, Atlanta, Georgia, USA, June 14-19 2009 Conference Web Site: http://cnd.memphis.edu/ijcnn2009/ Special Session Web Site: http://www.disi.unige.it/person/MasulliF/conferences/IJCNN2009-SS.html Description and Scope: The body of information surrounding molecular and genomic experiments and clinical investigations is rapidly growing as the magnitude and rate of applications involving large-scale high-throughput technologies are ever-increasing. Bioinformatic data mining efforts now range from more recent methods including miRNA target identification and protein structure prediction to classical methods such as ANN and RBFN classification of DNA microarray gene expression data. Data fusion and integration are also gaining considerable attention for merging signals, features, images, and text data from multiple sensors together in order to understand influences of data components on early detection and diagnosis of disease. Altogether, bioinformatics has become a very promising multidisciplinary research area in the life sciences because results provide new insights for interpretation and establish new leads for deeper understanding. Each year there are numerous Soft Computing and Machine Learning algorithms introduced providing new examples of application in related fields (clustering, feature selection, text mining, signal and image processing, data visualization, etc.). This session will take stock in new soft computing methods for bioinformatic data mining in general, and Neural Network methods in particular. Topics: We welcome papers which present novel algorithms or refined classical methods for the analysis of high dimensional bioinformatic data sets. The target problems include but are not limited to: * Data integration and fusion * Ensemble techniques * Biological sequence identification * DNA/CGH/SNP/miRNA arrays * Gene regulatory and ontology networks * Protein-protein, protein-small molecule interactions * Protein structure prediction * Cellular metabolism and signaling * Pharmacogenomics and pharmacodynamics * Metabolic pathways * Signal processing * Unsupervised and supervised classification * Imaging/data visualization * Text mining methods * Biomarker selection Organizers: Alexandru Floares (1), Francesco Masulli (2,3), (1) Department of Artificial Intelligence Oncological Institute Cluj-Napoca 400015 Str. Republicii, Nr. 34-36, Cluj-Napoca Romania E-mail: alexandru.floares iocn.ro (2) DISI Dept. Computer and Information Sciences University of Genova Via Dodecaneso 35 16146 Genoa, Italy E-mail: masulli disi.unige.it (3) Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, 1900 N 12th Street Philadelphia, PA 19122, USA. Important dates: As soon as possibile: Inform by email the Special Session organizers of your willness to submit a paper Paper submission deadline: December 15, 2008 (&) Author notification of acceptance or rejection: Gennuary 30, 2009 Deadline for final paper re-submission: March 10, 2009 (&&) (&) Paper submission (deadline Dec 15, 2008): At http://cnd.memphis.edu/ijcnn2009/submission.html you'll find the Instruction for Authors and the link to the IJCNN 2009 submission site. After uploaded your paper on the IJCNN 2009 submission site, send by email to the special session organizers a copy of your paper. In the Subject of the email please specify: "Paper submitted to SS on Bioinformatics IJCNN09". (&&) Final Paper re-submission (deadline March 10, 2009): After re-uploaded your paper on the IJCNN 2009 submission site, send by email to the special session organizers a copy of your revised paper and a letter indicating in detail all changes made. In the Subject of the email please specify: "Paper submitted to SS on Bioinformatics IJCNN09 (revised)". ------------------------------------------------------- -- <--------------------------------------------------------------------> Dr. Francesco Masulli Associate Professor of Computer Science DISI - Dept. Computer and Information Sciences University of Genova - Via Dodecaneso 35, 16146 Genoa - ITALY tel. +39 010 353 6604 fax. +39 010 353 6699 and Adjunct Associate Professor Center for Biotechnology - College of Science and Technology -Temple University - Philadelphia - PA, USA. email: masulli at disi.unige.it skype id: masulli url: http://www.disi.unige.it/person/MasulliF <--------------------------------------------------------------------> From boris.steipe at utoronto.ca Wed Nov 26 17:33:39 2008 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Wed, 26 Nov 2008 17:33:39 -0500 Subject: [BiO BB] Save protein structure image as an adobe SVG format file In-Reply-To: References: <1226534454.491b6e36e7d14@webmail.upv.es> <1226946262.4921b6d6b14d5@webmail.upv.es> <1227118784.492458c03ec5a@webmail.upv.es> <3E951E84-BE5A-42AC-A31F-BB16E240D52F@utoronto.ca> Message-ID: <2849EC40-0DE9-49B1-9657-59350FDF1B41@utoronto.ca> > Spheres aren't that hard for z-sorting, Yes, a collection of atoms can be well approximated with a Z-sorted stack of circles in 2D. But *molecules* are represented by intersecting spheres and the line of intersection is a circle at an arbitrary orientation relative to the viewer. It projects as an ellipse, and part of the ellipse is occluded. Think "methane". (And working with ball and stick models, or even cartoon or mesh representations, you'll start recoding much of what the 3D-viewer is there to do in the first place.) BKchem is 2D chemical structure editor. Again: Molscript produces postscript output. Postscript can be converted to svg. :-) B. On 25-Nov-08, at 9:17 AM, Mike Marchywka wrote: >> From: boris.steipe at utoronto.ca >> Date: Mon, 24 Nov 2008 21:15:03 -0500 >> To: bbb at bioinformatics.org >> Subject: Re: [BiO BB] Save protein structure image as an adobe SVG >> format file >> >> Meh. >> Simple Z-sorting is not intersecting spheres. >> If it's any non-trivial vector graphic representation you are trying >> to do, you might consider the following workflow: >> 3D-viewer -> View Matrix -> Molscript -> PS -> ps2svg > > there is something called bkchem, > > http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/ > Structure_drawing > > and if you look at discussions the viewers don't obviously have svg > output options. > > Certainly if you can't find direct svg output, conversion from > another model-preserving > output format would be great. But, I wouldn't dismiss the script > approach immediately > depending on your ultimate goals. A scriptable viewer could > generate many views but you > could also write a script without the viewer. > > Spheres aren't that hard for z-sorting, > > > http://en.wikipedia.org/wiki/Bounding_volume > > > > > > > > > >> >> >> B. >> >> >> >> >> On 24-Nov-08, at 7:23 PM, Mike Marchywka wrote: >> >>> >>> I guess the real question is, " what are you trying to do?" You >>> could >>> probably write a perl script to do this. The pdb is ascii, you just >>> need to project >>> 3D onto 2D and get some atom colors and radii. SVG AFAIK is all >>> ascii >>> XML which is easy to generate from a script. >>> If you take all the atoms, project, sort on Z ( distance from >>> viewer), >>> and generat XML that would probably give you what you need. >>> http://www.w3.org/Graphics/SVG/ >>> >>> the code to draw circles is pretty simple, >>> http://www.w3.org/TR/SVG11/shapes.html> Date: Tue, 25 Nov 2008 >>> 07:36:35 +0800> From: shreyasee.pradhan at gmail.com> To: >>> bbb at bioinformatics.org> Subject: Re: [BiO BB] Save protein >>> structure image as an adobe SVG format file>> Hi,>> For viewing >>> PDB files you can use Swiss PDB viewer software. Its free !!!>>> >>> On Fri, Nov 21, 2008 at 11:14 PM, Xiaowei Jiang >>> wrote:>>> Hi fellows,>>>> Does anyone >>> know a PDB viewer software or a way, in which I can save image>> >>> directly as an adobe SVG format file?>>>> Thanks in advance!!>>> >>>> Cheers,>> Xiaowei>>>>>>>>>> >>> _______________________________________________>> BBB mailing >>> list>> BBB at bioinformatics.org>> http://www.bioinformatics.org/ >>> mailman/listinfo/bbb>>>>>> --> Thanks,> Shreyasee> >>> _______________________________________________> BBB mailing list> >>> BBB at bioinformatics.org> http://www.bioinformatics.org/mailman/ >>> listinfo/bbb >>> _________________________________________________________________ >>> Proud to be a PC? Show the world. Download the ?I?m a PC? Messenger >>> themepack now. >>> hthttp://clk.atdmt.com/MRT/go/119642558/direct/01/ >>> _______________________________________________ >>> BBB mailing list >>> BBB at bioinformatics.org >>> http://www.bioinformatics.org/mailman/listinfo/bbb >> >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb > _________________________________________________________________ > Get more done, have more fun, and stay more connected with Windows > Mobile?. > http://clk.atdmt.com/MRT/go/119642556/direct/01/ > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From me_lily at msn.com Wed Nov 26 21:59:31 2008 From: me_lily at msn.com (lily) Date: Thu, 27 Nov 2008 02:59:31 +0000 Subject: [BiO BB] how to build pathway from microarray data Message-ID: hello all, I am new to pathway analysis. I have some microarray data and want to get some pathway. Would you please tell me how I can start? Thank you. _________________________________________________________________ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us From kiekyon.huang at gmail.com Fri Nov 28 08:27:55 2008 From: kiekyon.huang at gmail.com (Kie Kyon Huang) Date: Fri, 28 Nov 2008 21:27:55 +0800 Subject: [BiO BB] protein function prediction using protein interaction network Message-ID: hi everyone, i would like to know if anyone knows of software that can infer function for uncharacterised gene using protein interaction network? thanks Huang From kiekyon.huang at gmail.com Sat Nov 29 03:53:05 2008 From: kiekyon.huang at gmail.com (Kie Kyon Huang) Date: Sat, 29 Nov 2008 16:53:05 +0800 Subject: [BiO BB] orthologs Message-ID: how do we differentiate between true homologs and random sequences from the blast result?