From ngadewal at yahoo.com Tue Oct 5 02:10:28 2010 From: ngadewal at yahoo.com (nikhil gadewal) Date: Mon, 4 Oct 2010 23:10:28 -0700 (PDT) Subject: [BiO BB] monomer to trimer Message-ID: <783274.92660.qm@web51506.mail.re2.yahoo.com> Dear Users, ????????? I would like to convert the?monomer pdb structure into trimer?structure. Anyone know the online tool?which does this job. Thanks in advance. Nikhil From dan.bolser at gmail.com Thu Oct 7 03:46:12 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 7 Oct 2010 08:46:12 +0100 Subject: [BiO BB] monomer to trimer In-Reply-To: <783274.92660.qm@web51506.mail.re2.yahoo.com> References: <783274.92660.qm@web51506.mail.re2.yahoo.com> Message-ID: If the trimer is part of the crystal structure, you can find it in PISA: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.htm If the required symmetry operations are not present in the PDB file, you'll have to model the trimer... not sure of any online tool to to that... The best place for such questions is pdb-l (CC'ed), but please do post your findings back to the Bioinformatics.Org Forum. Cheers, Dan. On 5 October 2010 07:10, nikhil gadewal wrote: > Dear Users, > > ????????? I would like to convert the?monomer pdb structure into > trimer?structure. Anyone know the online tool?which does this job. > > Thanks in advance. > > Nikhil > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From ilonak at post.tau.ac.il Thu Oct 7 04:50:51 2010 From: ilonak at post.tau.ac.il (ilonak at post.tau.ac.il) Date: Thu, 07 Oct 2010 10:50:51 +0200 Subject: [BiO BB] pdb-l: monomer to trimer In-Reply-To: References: <783274.92660.qm@web51506.mail.re2.yahoo.com> Message-ID: <20101007105051.20254emaicfgasbv@webmail.tau.ac.il> Hi Nikhil, If you need to model a trimer given a monomer, you can try SymmDock: http://bioinfo3d.cs.tau.ac.il/SymmDock/ Hope this helps, Ilona -- Ilona Kifer Wolfson Structural Bioinformatics Lab Tel Aviv University Israel Quoting "Dan Bolser" : > If the trimer is part of the crystal structure, you can find it in PISA: > > http://www.ebi.ac.uk/msd-srv/prot_int/pistart.htm > > > If the required symmetry operations are not present in the PDB file, > you'll have to model the trimer... not sure of any online tool to to > that... > > The best place for such questions is pdb-l (CC'ed), but please do post > your findings back to the Bioinformatics.Org Forum. > > > Cheers, > Dan. > > On 5 October 2010 07:10, nikhil gadewal wrote: >> Dear Users, >> >> ????????? I would like to convert the?monomer pdb structure into >> trimer?structure. Anyone know the online tool?which does this job. >> >> Thanks in advance. >> >> Nikhil >> >> >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . > From emartz at microbio.umass.edu Thu Oct 7 19:16:43 2010 From: emartz at microbio.umass.edu (Eric Martz) Date: Thu, 07 Oct 2010 19:16:43 -0400 Subject: [BiO BB] pdb-l: monomer to trimer In-Reply-To: <20101007105051.20254emaicfgasbv@webmail.tau.ac.il> References: <783274.92660.qm@web51506.mail.re2.yahoo.com> <20101007105051.20254emaicfgasbv@webmail.tau.ac.il> Message-ID: <201010072318.o97NIOod024031@marlin.bio.umass.edu> Dear Nikhil, If the authors specify the trimer in REMARK 350 in the PDB file header, you can generate it with Michael Palmer's MakeMultimer.py server: http://watcut.uwaterloo.ca/cgi-bin/makemultimer/ The output of MakeMultimer names each chain differently, and all chains are placed in a single model. This makes it easier to use, in most common visualization software, than the multimers generated as "biological units" at rcsb.org, which have each chain in a separate model, and give them all the same name (e.g. chain A). There is an overview of methods for generating multimers within FirstGlance in Jmol: http://firstglance.jmol.org/notes.htm#pqs -Eric > > On 5 October 2010 07:10, nikhil gadewal wrote: > >> Dear Users, > >> > >> I would like to convert the monomer pdb structure into > >> trimer? structure. Anyone know the online tool which does this job. > >> > >> Thanks in advance. > >> > >> Nikhil /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://Martz.MolviZ.Org Top Five 3D MolVis Technologies http://Top5.MolviZ.Org FirstGlance, used by Nature - http://firstglance.jmol.org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.molviz.org Workshops: http://workshops.molviz.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://list.molviz.org Protein Explorer - 3D Visualization: http://proteinexplorer.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ From glen at ebi.ac.uk Fri Oct 8 03:30:28 2010 From: glen at ebi.ac.uk (Glen van Ginkel) Date: Fri, 08 Oct 2010 08:30:28 +0100 Subject: [BiO BB] monomer to trimer In-Reply-To: <783274.92660.qm@web51506.mail.re2.yahoo.com> References: <783274.92660.qm@web51506.mail.re2.yahoo.com> Message-ID: <4CAEC894.3090507@ebi.ac.uk> Unfortunately the link to PDBePISA is not correct. It should end in ".html". The PDBe has tinyURLs for all its services so you could use this instead... http://pdbe.org/pisa Regards Glen Quoting "Dan Bolser" : > > If the trimer is part of the crystal structure, you can find it in PISA: > > > > http://www.ebi.ac.uk/msd-srv/prot_int/pistart.htm > > > > > > If the required symmetry operations are not present in the PDB file, > > you'll have to model the trimer... not sure of any online tool to to > > that... > > > > The best place for such questions is pdb-l (CC'ed), but please do post > > your findings back to the Bioinformatics.Org Forum. > > > > > > Cheers, > > Dan. > > nikhil gadewal wrote: > Dear Users, > > I would like to convert the monomer pdb structure into > trimer structure. Anyone know the online tool which does this job. > > Thanks in advance. > > Nikhil > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > From paolo.romano at istge.it Tue Oct 12 03:53:10 2010 From: paolo.romano at istge.it (Paolo Romano) Date: Tue, 12 Oct 2010 09:53:10 +0200 Subject: [BiO BB] NETTAB 2010 Biological Wikis: Call for posters and participation Message-ID: <201010120754.o9C7rBJB014425@clus2.istge.it> Apologizes for duplications === Joint NETTAB 2010 and BBCC 2010 workshop Biological Wikis November 29 - December 1, 2010 Congress Center, University of Naples "Federico II", Naples, Italy http://www.nettab.org/2010/ The joint NETTAB and BBCC 2010 workshop on "Biological Wikis" promises to be a great meeting for all researchers involved in the exploitation of wikis in biology. Come and discuss your ideas and doubts with such scientists as Alex Bateman, Alexander Pico, Andrew Su, Dan Bolser, Robert Hoffmann, Thomas Kelder, Mike Cariaso, Adam Godzik, Luca Toldo and many other who, we hope, will join the workshop. It's a great chance to follow smart tutorials and lectures on WikiPathways, WikiGenes, Semantic Wiki, PDBWiki, Gene Wiki and a proficient use of Wikipedia. See a list of keynote speakers and tutorials at http://www.nettab.org/2010/progr.html . There still is time to submit abstracts for posters and software demonstrations until next October 17, 2010! The complete Call is available on-line at http://www.nettab.org/2010/call.html . Registration is open at http://www.nettab.org/2010/rform.html . Register within next October 29, 2010 and take profit of early registration fees. A reduction of 20 euro applies to all fees for members of ISCB and other societies and networks. More reductions are foreseen for PhD students. Further information is availble at http://www.nettab.org/2010/ . Looking forward to seeing you soon in Naples. Paolo Romano Paolo Romano (paolo.romano at istge.it) Bioinformatics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 Skype: p.romano Web: http://www.nettab.org/promano/ From denguehost at gmail.com Tue Oct 12 21:36:33 2010 From: denguehost at gmail.com (Chris Baker) Date: Tue, 12 Oct 2010 22:36:33 -0300 Subject: [BiO BB] CFP: BMC Bioinformatics Special Issue - ECCB 2010 Workshop AIMM Message-ID: Apologies for cross postings OPEN CALL FOR PAPERS - BMC Bioinformatics Special Issue ================================================= Following the Event: ================ ECCB Workshop: http://www.eccb2010.org/index.php/workshops/workshop2 AIMM2010 Annotation, Interpretation and Management of Mutations http://www.unbsj.ca/sase/csas/data/aimm2010/ A call for papers is now open to all workshop participants and newcomers who could not attend the AIMM 2010 event. See the link below for details of the Special Issue on the AIMM Theme. AIMM Themes =========== Mutation Nomenclature, Databases and Metadata: Design, Content, Accuracy. Extraction of mutations and annotations from literature. Impacts of Mutations: Prediction and Bootstrapping. Mutation Data Integration, Phenotype Ontologies, Semantic Support and Reuse. Other related topics will be considered http://www.unbsj.ca/sase/csas/data/aimm2010/themes.html Dates ===== Submissions open October 10th (2010) Abstracts Due November 30th (2010) Submissions due* December 18th (2010) Revised manuscript submitted February 28th (2011) CFP BMC Bioinformatics Page http://www.unbsj.ca/sase/csas/data/aimm2010/bmc.html Any further questions can be sent to bakerc at unb.ca Best regards, Christopher Baker Rene Witte Dietrich Rebholz-Schuhmann -- Christopher J. O. Baker Ph. D. Associate Professor Dept. Computer Science and Applied Statistics University of New Brunswick, Canada http://ca.linkedin.com/in/christopherjobaker From tridibd at pitt.edu Thu Oct 14 10:07:49 2010 From: tridibd at pitt.edu (tridibd at pitt.edu) Date: Thu, 14 Oct 2010 10:07:49 -0400 Subject: [BiO BB] help req with Vienna RNA package Message-ID: <336d75cf555ee5f1e6336c07a92212d2.squirrel@webmail.pitt.edu> Hello all, I am not a student at Univ. Pitt. The following question is related to my research. I am new to computational biology and so if I may be asking a very naive question, but the information is crucial for me right now. I would like to extract the numerical values of the base-pair probabilities from the dot plot generated by RNAfold in Vienna RNA package. According to the manual, the area of the dots are proportional to the base pair probabilities. But I am not sure this helps. Visually it gives some idea but I want to see how the base pair probabilities are affected on single point mutations of a long RNA seq ( > 500 nt long). Any help regarding this will be greatly appreciated. Thanks, Tridib From erik at q32.com Sun Oct 17 12:46:14 2010 From: erik at q32.com (Erik Aronesty) Date: Sun, 17 Oct 2010 12:46:14 -0400 Subject: [BiO BB] help req with Vienna RNA package In-Reply-To: <336d75cf555ee5f1e6336c07a92212d2.squirrel@webmail.pitt.edu> References: <336d75cf555ee5f1e6336c07a92212d2.squirrel@webmail.pitt.edu> Message-ID: Might want to use RNAplfold for that, right? http://www.tbi.univie.ac.at/~ivo/RNA/RNAplfold.html On Thu, Oct 14, 2010 at 10:07 AM, wrote: > Hello all, > > I am not a student at Univ. Pitt. The following question is related to my > research. I am new to computational biology and so if I may be asking a > very naive question, but the information is crucial for me right now. From rwagner at faw.jku.at Mon Oct 18 07:08:01 2010 From: rwagner at faw.jku.at (Roland Wagner) Date: Mon, 18 Oct 2010 13:08:01 +0200 Subject: [BiO BB] ITBAM 2011: Call for Papers Message-ID: <4CBC2A91.9080803@faw.jku.at> */Preliminary Call for Papers and Posters/* * * *International Conference on* * * Information Technology in Bio- and Medical Informatics ITBAM 2011 In conjunction with DEXA 2011 www.dexa.org 29 August -- 2 September 2011, Toulouse, France Data intensive disciplines like life sciences and medicine are promoting vivid research activities in the area of databases. Modern technologies such as high-throughput mass-spectrometry and sequencing, micro-arrays, high-resolution imaging, etc. produce enormous and continuously increasing amounts of data. Huge public databases provide access to aggregated and consolidated information on genome and protein sequences, biological pathways, diseases, anatomy atlases, and scientific literature. There has never been more potentially available information to study biomedical systems ranging from single cells to complete organisms. However, it is a non-trivial task to transform the vast amount of biomedical data into actionable information triggering scientific progress and supporting patient management. Major biomedical application scenarios for research in the database community include but are not limited to: ? Systems biology, ? Genomics, proteomics, and metabolomics, ? Genome-wide association studies, * Drug target discovery and personalized medicine, ? Neuroscience, * Electronic patient records, ? Patient monitoring, ? Surgery planning and support, ? etc. Various emerging database technologies for coping with the challenges of these application scenarios have been developed and are an active area of research in information technology: ? Administration of vast amounts of data, ? Integration of heterogeneous data sources, ? Federated and distributed databases, ? Data warehouses, ? Data mining techniques like classification, clustering, association rule mining, etc. ? Decision support systems, ? Information and image retrieval, ? Signal processing and streaming databases, ? Privacy protection and data security, ? Data quality assurance, ? Process management and collaborative work, ? User interfaces and visualization, ? etc. Designing database technology to support applications in life sciences and medicine is an inspiring field of interdisciplinary research. Often there is a long way from an idea to practical application which involves intensive discussion between experts in information technology, life sciences and medicine. ITBAM accompanies and supports this way by providing an excellent venue for the exchange of ideas, fruitful discussion, and effective interaction among interdisciplinary researchers. In addition to the regular conference program featuring presentations of full and short research papers published in the proceedings, ITBAM encourages the submission of posters reporting work in progress. All accepted posters will be displayed during the whole event and abstracts will also be included in the proceedings. Important Dates: ITBAM conference papers and poster submissions: ? Paper submission deadline (firm): March 7, 2011 ? Notification of acceptance: May 11, 2011 ? Poster submission deadline (firm): May 16, 2011 ? Camera-ready copies due: June 9, 2011 Paper Submission Details: Authors are invited to submit electronically original contributions or experience reports in English. The submitted manuscript should closely reflect the final paper as it will appear in the proceedings. ? Paper submissions should not exceed 15 pages in LNCS format. Poster submissions are expected to consist of 1 page Abstract (http://www.springer.de/comp/lncs/authors.html). ? Any submission that exceeds length limits or deviates from formatting requirements may be rejected without review. ? For registration and electronic submission see: http://confdriver.ifs.tuwien.ac.at/ ? The submission system will be open starting from January 2011. ? Submitted papers will be carefully evaluated based on originality, significance, technical soundness, and clarity of exposition. ? Duplicate submissions are not allowed. Authors are expected to agree to the following terms: "I understand that the paper being submitted must not overlap substantially with any other paper that I am a co-author of and that is currently submitted elsewhere. Furthermore, previously published papers with any overlap are cited prominently in this submission." Accepted Papers: All accepted conference papers will be published in "Lecture Notes in Computer Science" (LNCS) by Springer Verlag. Accepted full papers will be of 15 pages length, short papers 8 pages. Authors of accepted papers must sign a Springer copyright release form. For further inquiries, please contact the Conference Organisation Office (gabriela at dexa.org). * * *General Chairperson: * Christian B?hm, University of Munich, Germany *Program Committee Co-chairpersons:* Sami Khuri, San Jos? State University, USA Lenka Lhotska, Czech Technical University Prague, Czech Republic Nadia Pisanti, University of Pisa, Italy *Program Committee:* tbd From jeff at bioinformatics.org Wed Oct 20 21:43:20 2010 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 20 Oct 2010 21:43:20 -0400 Subject: [BiO BB] SHORT CONFERENCE: Bioinformatics to Systems Biology 2010 Message-ID: <4CBF9AB8.4070400@bioinformatics.org> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- SHORT CONFERENCE Bioinformatics to Systems Biology 2010 Online at Bioinformatics.Org Friday, October 22, 2010, 13:00-15:00 GMT http://www.bioinformatics.org/wiki/BSB10 LIVE: http://www.livestream.com/bifx -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- The BSB series is for students and those in the research community who fall under broader disciplines of bioinformatics and systems biology, and the BSB '10 conference will include invited talks within the sub-disciplines of these two exciting fields. Speakers: * Professor Keith Dunker, Indiana University, "Bioinformatics and Intrinsically Disordered Proteins" * Dr. Lars Juhl Jensen, University of Copenhagen, "Protein Networks: Basis for Large-Scale Data Mining" * Dr. Dan Bolser, University of Dundee, "Community Annotation and BioWikis" * Dr. L Aravind, NCBI-Bethesda (TBA) Registration: Registering on the Bioinformatics.Org education site will provide you with links to downloadable lecture videos and also permit communication beyond the Livestream broadcast. * Employer (for-profit & government): USD 30.00 * Employer (non-profit & academic): USD 20.00 (also for students in developed countries) * Yourself (not being reimbursed): USD 10.00 (also for students in developing countries) Online: http://www.bioinformatics.org/edu/BSB10 Mail-in: http://www.bioinformatics.org/edu/download/edu_registration.pdf From prasanna at gmail.com Sat Oct 23 23:10:59 2010 From: prasanna at gmail.com (Prasanna Desikan) Date: Sat, 23 Oct 2010 22:10:59 -0500 Subject: [BiO BB] CFP: Second Workshop on Data Mining for Healthcare Management (DMHM 2011) Message-ID: ** Please feel to circulate to relevant interested groups *** *********************************************************************** CFP: Second Workshop on Data Mining for Healthcare Management Held in conjunction with The 15th Pacific-Asia Conference on Knowledge Discovery and Data Mining 24-27 May 2011 (Tue-Fri) - Shenzen, China http://www.cs.umn.edu/~desikan/pakdd2011/dmhm.html ************************************************************************ ----------------------------------------------------------- Important Dates ----------------------------------------------------------- Paper Submission Deadline: 10 December, 2010 (Friday) Author Notification: 21 January, 2011 (Friday) Camera-Ready Deadline: 18 February, 2011 (Friday). ----------------------------------------------------------- Workshop Scope ----------------------------------------------------------- DMHM 2011 encourages the following topics (but is not limited to) related to application of data mining techniques to healthcare: # Theoretical foundations in Data Mining # Data models for healthcare management # Patient management # Medical decision making # Medical diagnosis # Evidence based medicinal decisions # Medical Insurance Fraud Detection # Patient Flow Models in Hospitals # Clinical data analysis # Cloud-computing models and challenges for healthcare. # Privacy and security in healthcare. # Improving Quality of products and services # Data collection and integration techniques # Data cleaning and transformation # Knowledge based medical recommendation models # Information visualization of medical data. # Enhancing quality of tools available to healthcare providers. # Medical device fault detection and prevention. # Reliability of medical devices. # Pattern recognition in medical images and data. ----------------------------------------------------------- Program Committee ----------------------------------------------------------- Vipin Kumar, University of Minnesota Joydeep Ghosh, University of Texas, Austin Wei Jiang, Institute of Engineering and Logistics Management, Hong Kong VRK Subrahmanya Rao, Cognizant Technologies Hui Xiong, Rutgers University Michael Steinbach, University of Minnesota Deepa Mahajan, Boston Scientific Yonghong Tian, Peking University Woong-Kee Loh, Sungkyul University Tieyun Qian, Wuhan University Kalyan Pamarthy, Medtronic Jimmy LIU Jiang, iMED(Institute for Infocomm Research (I2R)) Chandan Reddy, Wayne State University San-Yih Hwang, National Sun Yat-Sen University ----------------------------------------------------------- Workshop Organization Chairs ----------------------------------------------------------- Dr. Prasanna Desikan Cardiac Device Telematics Boston Scientific Prof. Jaideep Srivastava Computer Science & Engineering University of Minnesota Prof. Ee-Peng Lim School of Information Systems Singapore Management University ----------------------------------------------------------- ** Please check the website for any details and latest information ** For any further questions please contact Prasanna at prasanna [at] gmail [dot] com From ngadewal at yahoo.com Wed Oct 27 03:37:54 2010 From: ngadewal at yahoo.com (nikhil gadewal) Date: Wed, 27 Oct 2010 00:37:54 -0700 (PDT) Subject: [BiO BB] Gene Ontology Message-ID: <795192.33155.qm@web51505.mail.re2.yahoo.com> Dear All, I have a list of genes with?gene symbol (entrez) which has to be annotated by gene ontology. I am looking for online tool which takes?genelist as input and will give output?the genes which?are involved in bioloical process and molecular funtion. For eg. Out of 100 genes (genelist) submitted, will give output say 30 genes are involved in "Signal transduction" (biological process). If anyone know such kind of tool than please let me know. Thankyou in advance. Nikhil From marty.gollery at gmail.com Wed Oct 27 14:33:10 2010 From: marty.gollery at gmail.com (Martin Gollery) Date: Wed, 27 Oct 2010 11:33:10 -0700 Subject: [BiO BB] Gene Ontology In-Reply-To: <795192.33155.qm@web51505.mail.re2.yahoo.com> References: <795192.33155.qm@web51505.mail.re2.yahoo.com> Message-ID: Try a uniprot search at http://www.uniprot.org/ under 'field' pick Gene Ontology, then under 'term' type 'signal transduction'. Marty Gollery On Wed, Oct 27, 2010 at 12:37 AM, nikhil gadewal wrote: > Dear All, > > I have a list of genes with?gene symbol (entrez) which has to be annotated by > gene ontology. > > I am looking for online tool which takes?genelist as input and will give > output?the genes which?are involved in bioloical process and molecular funtion. > For eg. Out of 100 genes (genelist) submitted, will give output say 30 genes are > involved in "Signal transduction" (biological process). > If anyone know such kind of tool than please let me know. > Thankyou in advance. > > Nikhil > > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist Tahoe Informatics www.bioinformaticist.biz www.hiddenmarkovmodels.com From marchywka at hotmail.com Wed Oct 27 14:59:43 2010 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 27 Oct 2010 14:59:43 -0400 Subject: [BiO BB] Gene Ontology In-Reply-To: <795192.33155.qm@web51505.mail.re2.yahoo.com> References: <795192.33155.qm@web51505.mail.re2.yahoo.com> Message-ID: ---------------------------------------- > Date: Wed, 27 Oct 2010 00:37:54 -0700 > From: ngadewal at yahoo.com > To: bbb at bioinformatics.org > Subject: [BiO BB] Gene Ontology > > Dear All, > > I have a list of genes with gene symbol (entrez) which has to be annotated by > gene ontology. > > I am looking for online tool which takes genelist as input and will give > output the genes which are involved in bioloical process and molecular funtion. > For eg. Out of 100 genes (genelist) submitted, will give output say 30 genes are > involved in "Signal transduction" (biological process). > If anyone know such kind of tool than please let me know. > Thankyou in advance. There may be specific tools for this but one option is eutils. http://eutils.ncbi.nlm.nih.gov/ ?For example,I have a script that can go search the gene db and return and xml file with an entry for each gene of interest. You can then parse or do whatever you want to associate attributes with each gene and pick the ones you want. If I type this, eutilsnew -v -out xxx -gene human I get a bunch of genes in "xxx" that relate to the search term "human". Apparently there is a field called Prot-ref_desc that is close to what you want but you would need to look a little more - not sure if looking up protein would be needed to get classification you want etc. more xxx | grep "track_geneid\|rot-ref_desc" ????? 253461 ????? zinc finger and BTB domain-containing protein 38 ????? 55245 ????? ubiquinol-cytochrome c reductase complex chaperone CBP3 hom olog ????? 8353 ????? histone H3.1 ????? 8091 ????? high mobility group protein HMGI-C ????? 79145 ????? coiled-coil-helix-coiled-coil-helix domain-containing prote in 7 ????? 3007 ????? histone H1.3 ????? 195814 ????? epidermal retinol dehydrogenase 2 ????? 57211 ????? G-protein coupled receptor 126 ????? 57188 ????? ADAMTS-like protein 3 > > Nikhil > > From pandey.gaurav at gmail.com Wed Oct 27 15:22:51 2010 From: pandey.gaurav at gmail.com (Gaurav Pandey) Date: Wed, 27 Oct 2010 12:22:51 -0700 Subject: [BiO BB] Gene Ontology In-Reply-To: <795192.33155.qm@web51505.mail.re2.yahoo.com> References: <795192.33155.qm@web51505.mail.re2.yahoo.com> Message-ID: The DAVID tool (http://david.abcc.ncifcrf.gov/) is one of the best for this task. Also, Gene Ontology itself has several annotation tools listed at http://www.geneontology.org/GO.tools.microarray.shtml. I'll be happy to help out more if contacted directly. Gaurav On Wed, Oct 27, 2010 at 12:37 AM, nikhil gadewal wrote: > Dear All, > > I have a list of genes with gene symbol (entrez) which has to be annotated > by > gene ontology. > > I am looking for online tool which takes genelist as input and will give > output the genes which are involved in bioloical process and molecular > funtion. > For eg. Out of 100 genes (genelist) submitted, will give output say 30 > genes are > involved in "Signal transduction" (biological process). > If anyone know such kind of tool than please let me know. > Thankyou in advance. > > Nikhil > > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Gaurav Pandey Email: gaurav at compbio.berkeley.edu Plant & Molecular Biology Department Webpage: compbio.berkeley.edu/people/gaurav University of California, Berkeley Tel: 612-701-2494 From stan.gaj at maastrichtuniversity.nl Thu Oct 28 11:41:56 2010 From: stan.gaj at maastrichtuniversity.nl (Gaj Stan (BIGCAT)) Date: Thu, 28 Oct 2010 17:41:56 +0200 Subject: [BiO BB] Gene Ontology In-Reply-To: References: <795192.33155.qm@web51505.mail.re2.yahoo.com> Message-ID: You could also try out GO-Elite ( http://www.genmapp.org/go_elite/ ) with all filter settings turned off, since you don't need that for your specific question. If you need a hand with this tool, just give a shout! Best, -- Stan -----Original Message----- From: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org] On Behalf Of Gaurav Pandey Sent: Wednesday, October 27, 2010 9:23 PM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Gene Ontology The DAVID tool (http://david.abcc.ncifcrf.gov/) is one of the best for this task. Also, Gene Ontology itself has several annotation tools listed at http://www.geneontology.org/GO.tools.microarray.shtml. I'll be happy to help out more if contacted directly. Gaurav On Wed, Oct 27, 2010 at 12:37 AM, nikhil gadewal wrote: > Dear All, > > I have a list of genes with gene symbol (entrez) which has to be annotated > by > gene ontology. > > I am looking for online tool which takes genelist as input and will give > output the genes which are involved in bioloical process and molecular > funtion. > For eg. Out of 100 genes (genelist) submitted, will give output say 30 > genes are > involved in "Signal transduction" (biological process). > If anyone know such kind of tool than please let me know. > Thankyou in advance. > > Nikhil > > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Gaurav Pandey Email: gaurav at compbio.berkeley.edu Plant & Molecular Biology Department Webpage: compbio.berkeley.edu/people/gaurav University of California, Berkeley Tel: 612-701-2494 _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb