From suzi at berkeleybop.org Wed May 2 16:50:41 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Wed, 2 May 2007 16:50:41 -0700 Subject: [gofriends] Berkeley (GO et al.) is looking to hire Message-ID: <8C4B8E48-7EC8-4689-801C-C10216DFBB21@berkeleybop.org> Hi all, We're hiring. It's gone from bust to boom in the space of a few months, and now we're scrambling to get 3 new people on board. I'm really sorry about the multiple postings, but we're trying to get the word out. from all of us at Berkeley... Suzi Lewis, Chris Mungall, Seth Carbon, John Day-Richter, Mark Gibson, Karen Eilbeck, & Nicole Washington Software Developer positions in Berkeley: http://berkeleybop.org/ content/jobs/ The Berkeley Bioinformatics and Ontologies Project (BBOP, http:// berkeleybop.org), located at Lawrence Berkeley National Laboratory (LBNL), is seeking three software developers to craft tools for the collection, annotation, and integration of biomedical data. The BBOP is a founding member of the Gene Ontology Consortium, and a part of the National Center for Biomedical Ontology. We have a long history developing open source software and databases for Drosophila and other model organisms, and are an original member of the Generic Model Organism Database (GMOD) project. We are an extremely collaborative team that is built upon the creative sharing of ideas among bright individuals. 1. modENCODE The applicant will work on an important new project, modENCODE, whose aim is to discover and explore the genomes of C. elegans and D. melanogaster , using new scientific strategies and new technologies for discovery. It is a collaborative project with Cold Spring Harbor Laboratory, Cambridge University, University of California Santa Cruz. The applicant will be responsible for collecting and collating experimental data from many different sources. [see http:// berkeleybop.org/content/jobs/modENCODE.shtml for more...] 2. NCBO/BIRN The applicant will work on an important new collaboration between the National Center for Biomedical Ontologies (NCBO) and the Biomedical Informatics Research Network (BIRN). The BIRN, based at the University of California San Diego, is an initiative within the National Institutes of Health that fosters large-scale collaborations in biomedical science by utilizing the capabilities of the emerging cyberinfrastructure. BIRN is targeting advances in understanding the genetics of human disease by identifying correlations between genetic insults and neuropathological processes. The database mediation software will support ontological query and retrieval of image information based on phenotypic descriptions. Our role is to assist in building the requisite data and knowledge stores, by building ontology-directed graphs for query navigation. [see http:// berkeleybop.org/content/jobs/BIRN.shtml for more ...] 3. APOLLO The applicant will work on an important software component of the GMOD project: Apollo. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert curation of the genome, all within a graphical environment. Our role is to support the global users of Apollo and to extend its capabilities in numerous ways. The Apollo project is a joint collaboration between LBNL and the Arabidopsis Information Resource (TAIR), located at Stanford. [ see http://berkeleybop.org/content/jobs/Apollo.shtml for more ...] How to Apply Applications and questions may be sent to Nicole Washington nlwashington at lbl.gov with the project code in the subject line. Please include a cover letter, resume, and contact information with your application. -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From elhamrose at yahoo.com Wed May 9 10:56:31 2007 From: elhamrose at yahoo.com (Elham Khabiri) Date: Wed, 9 May 2007 10:56:31 -0700 (PDT) Subject: [gofriends] a question Message-ID: <103235.90630.qm@web32214.mail.mud.yahoo.com> Hello every one. I plan to work with a measure to calculate the semantic similarity between genes or proteins and evaluate them with the sequence similarity measure like E-value and Bit Score taken from Blast tool of those gene/protein pairs. Does any body have a set ready like the following so that I can work with those genes and proteins to apply my measure on them? It is so difficult for me to get the bit score and e-value for 1000-2000 gene/protein pairs using the blast tool available online. The set that I need has the following format: Gene1 Gene2 E-value Bit score or Protein1 Protein 2 E-value Bit score I do appreciate it in advance. Elham --------------------------------- Ahhh...imagining that irresistible "new car" smell? Check outnew cars at Yahoo! Autos. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20070509/e36c2ae4/attachment.html From dbinns at ebi.ac.uk Wed May 9 15:57:27 2007 From: dbinns at ebi.ac.uk (David Binns) Date: Wed, 09 May 2007 23:57:27 +0100 Subject: [gofriends] a question In-Reply-To: <103235.90630.qm@web32214.mail.mud.yahoo.com> References: <103235.90630.qm@web32214.mail.mud.yahoo.com> Message-ID: <464251D7.6090609@ebi.ac.uk> Elham Khabiri wrote: > Hello every one. > > I plan to work with a measure to calculate the semantic similarity > between genes or proteins and evaluate them with the sequence > similarity measure like E-value and Bit Score taken from Blast tool of > those gene/protein pairs. The EBI runs a project called CluSTr which calculates E-values (from Smith-Waterman) for all pairs of sequences in UniProt Knowledgebase. Do contact John Maslen for more information - sample datasets can be provided by arrangement. Hope this helps, David Binns InterPro EBI -- David Binns EMBL-EBI 07919445300 -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From asidhu at biomap.org Sat May 12 14:59:58 2007 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Sun, 13 May 2007 07:59:58 +1000 Subject: [gofriends] CFP: 2nd IEEE International Workshop on Data Mining in Bioinformatics (DMB 2007) Message-ID: <1179007198.464638de30a8a@mail.opentransfer.com> 2nd International Workshop on Data Mining in Bioinformatics (DMB 2007) With IEEE/WIC/ACM WI-IAT-BIBM 2007 & IEEE GrC 2007 http://dmb07.swbio.org/ MOTIVATION Data Mining deals with the use of data analysis techniques and methodologies in the design, development and assessment of data and information systems for biomedical computing. The goal of this workshop is to share research solutions using data mining approaches to problems of today's biomedical systems and to identify new issues and directions for future research in biomedical data mining. Techniques and Methodologies proposed in this workshop will help addressing two major challenges to incorporate this vast biological knowledge into the data mining cycle: (i) designing efficient the data mining frameworks; and (ii) adapting existing data mining algorithms to understand constantly varying and changing biomedical data. In this workshop we hope to present to the audience, the state-of-the-art frameworks for bringing the background biomedical knowledge into the pattern recognition task for biomedical data. THEMES In DMB 2007, complementary to main themes of IEEE BIBM 2007, special focus is aimed at looking on the evolving areas of interest for Application of Data Mining in Bioinformatics, namely Semantic Biomedicine, Biomedical Privacy and Security, Biometrics and Health Informatics. Thus as part of DMB 2007, there are four special tracks on: 1. Biomedical Data Mining: Theory and Applications 2. Semantics in Biomedicine 3. Biomedical Privacy, Security and Biometric Authentication 4. Health Informatics IMPORTANT DATES August 10, 2007 Paper Submission Deadline September 10, 2007 Notification of acceptance September 17, 2007 Final camera-ready paper due November 2 - 5, 2007 Workshop Days TOPICS Authors are invited to submit original papers to the workshop exploring data mining theories, techniques, and applications for Bioinformatics. Papers are invited (but not limited) to the following topics: ? Biomedical Data Mining Theory and Applications o Genomics and Proteomics o Comparative Genomics o Microarray Data Analysis o Protein/RNA Structure Prediction o Phylogenetics o Drug Design o Feature selection and pattern discovery in biological data o Biomedical Literature Mining o System Biology and Pathways o Data mining applications in bioinformatics, biomedicine, health care and other biomedical domain areas ? Semantics in Biomedicine o Conceptual Models for Biological and Medical Data o Modeling of Biochemical Pathways o Biological Data Visualization o Biomedical Ontologies o Biomedical Data Engineering using Ontologies o Biological Database Management o Biomedical Data Warehousing o Interoperation of Biomedical Databases o Biomedical Query Processing, Query Optimization, and Information Retrieval ? Biomedical Data Privacy and Security o Trusted Systems for Biomedical Data Frameworks o Secure e-science protocols and web services o Soft Computing methods in biomedical privacy and security o Management of emerging health care technologies ? Heath Informatics o Electronic Health Records o Clinical Assessment and Patient Diagnosis o Disease Control and Prevention o Medical informatics o Clinical decision support design, development and implementation o e-health and m-health o Virtual health technologies PAPER SUBMISSION Please submit a full length paper (not exceeding 5000 words) thorough the online submission system (http://kis-lab.com/cyberchair/bibm07/scripts/submit.php). Electronic submissions (in PDF or Postscript format) are required. Selected participants will be asked to submit their revised papers in a format to be specified at the time of acceptance. Extended versions of selected papers will be published in a Special Issues of International Journal of Data Mining and Bioinformatics (IJDMB) and International Journal of Computer Systems Science & Engineering (CSSE). Selected high quality submissions will be published as book chapters in an edited book entitled: "Annual Review of Biomedical Knowledge Discovery and Data Mining: Enriching Biomedical Data Mining with Ontologies" in Studies in Computational Intelligence Series by Springer. For further questions, please contact technical program chair: dmb07 at swbio.org ORGANIZATION General Chairs: Tharam S. Dillon Curtin University of Technology, Australia Elizabeth Chang Curtin University of Technology, Australia Program Chairs: Amandeep S. Sidhu Curtin University of Technology, Australia Farookh K. Hussain Curtin University of Technology, Australia Steering Committee: ? Alexey Tysmbal (Siemens, Germany) ? Amandeep S. Sidhu (Curtin University of Technology, Perth, Australia) ? Elizabeth Chang (Curtin University of Technology, Perth, Australia) ? Farookh K. Hussain (Curtin University of Technology, Perth, Australia) ? Jake Chen (Indiana University, USA) ? Jason Wang (New Jersey Institute of Technology, USA) ? Mykola Pechenizkiy (Eindhoven University of Technology, Netherlands) ? Mohammed J. Zaki (Rensselaer Polytechnic Institute, USA) ? T. Y. Lin (San Jose State University, USA) ? Tharam S. Dillon (Curtin University of Technology, Perth, Australia) ? Tony Hu (Drexel University, USA) ? Yi Pan (Georgia State University, USA) Special Track Chairs: ? Biomedical Data Mining ? Tony Hu ? Semantics in Biomedicine ? Amandeep S. Sidhu ? Biomedical Privacy, Security and Biometric Authentication ? Farookh K. Hussain ? Health Informatics ? Maja Hadzic -- -- -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From trudy at vbi.vt.edu Mon May 14 09:57:43 2007 From: trudy at vbi.vt.edu (Trudy Torto-Alalibo) Date: Mon, 14 May 2007 12:57:43 -0400 Subject: [gofriends] VBI Genome Annotation workshop series Message-ID: <46489507.1080307@vbi.vt.edu> FYI: * VBI Genome Annotation workshop series* The Virginia Bioinformatics Institute (VBI) at Virginia Tech is organizing a series of workshops this summer under the direction of Professor Brett Tyler. The VBI Genome Annotation workshop series will host a Plant-Associated Microbe Gene Ontology (PAMGO) Training Workshop and an Oomycete Bioinformatics Training Workshop from August 8-10, 2007, and a Hyaloperonospora parasitica Genome Annotation Jamboree from August 12-17, 2007. The PAMGO and Oomycete Bioinformatics workshops will run concurrently from August 8-10. The first two days for both workshops will be dedicated to presentations on structural genomics and functional genomics including in-depth coverage of the Gene Ontology and the use of PAMGO terms in the annotation and analysis of gene products from microbes that associate with plant and animal hosts. Concurrent sessions will run on the third day. Session 1 will be devoted to hands-on exercises involving literature and sequence/structural similarity-based PAMGO annotations. Session 2 will cover resources and tools for annotation and analysis of oomycete genomic sequences. The Hyaloperonspora parasitica Annotation Jamboree will follow immediately on August 12-17. This will include presentations on the biology of /H. parasitica/, genomic resources available to date, tools for sequence annotation and analysis. Participants will then break into groups reflecting relevant subject areas for several days of manual annotation. There will be no registration fee and a limited number of fellowships of up to $500.00 will be available. For details on the workshops, including fellowship application and registration, visit: http://www.cpe.vt.edu/vbi-genome/ -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From dhowe at cs.uoregon.edu Mon May 14 10:46:07 2007 From: dhowe at cs.uoregon.edu (Doug howe) Date: Mon, 14 May 2007 10:46:07 -0700 Subject: [gofriends] Meeting Announcement - Second International Biocuration Meeting Message-ID: <4648A05F.7020507@cs.uoregon.edu> *Second Meeting Announcement* 2nd International Biocuration Meeting October 25-28, 2007 Dolce Hayes Mansion, San Jose, California, USA Registration Deadline: July 1, 2007 Purpose: The goal of this meeting is to provide a forum for curators and developers of biological databases to discuss their work, promote collaboration, and foster a sense of community in this important and rapidly growing area of research. Plenary Speakers: Helen Berman - PDB Minoru Kanehisa - KEGG Judy Blake - GO Focus Areas: Literature Collection and Curation Sequence Annotation and Comparative Genomics Ontologies Functional Genomics Curation Curation Standards and Best Practices Community Curation The First Biocuration Meeting was a great success. We have taken comments from the first meeting into consideration while planning this meeting. We look forward to your participation in a second successful meeting! Please take the time to register, as early registration will assist us with meeting planning. For more information and links to register or submit abstracts, please see the meeting web site at: http://biocurator.org/Mtg2007/ The meeting organizers would like to thank the Genetics Society of America, the National Science Foundation, the Klaus Tschira Foundation, and Bioneer for their support. Organizing Committee: Maria Costanzo -Saccharomyces and Candida Genome Databases, Stanford University, USA Petra Fey -dictyBase, Northwestern University, USA Takashi Gojobori -Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Japan Win Hide -South African National Bioinformatics Institute, University of the Western Cape, South Africa David Hill -Mouse Genome Informatics, USA Doug Howe -Zebrafish Information Network, University of Oregon, USA Renate Kania -Scientific Databases and Visualization, EML Research gGmbH, Germany Sue Rhee The Arabidopsis Information Resource, Carnegie Institution, USA Mary Schaeffer -USDA ARS , MaizeGDB and University of Missouri, USA Susan St. Pierre -Flybase, Harvard, USA Simon Twigger -Rat Genome Database, Medical College of Wisconsin at Milwaukee, USA Owen White -The Institute for Genomic Research, USA -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From Reactome-Knowledgebase at reactome.org Tue May 15 06:24:42 2007 From: Reactome-Knowledgebase at reactome.org (Reactome-Knowledgebase at reactome.org) Date: Tue, 15 May 2007 09:24:42 -0400 Subject: [gofriends] New version of Reactome knowledgebase released Message-ID: <000c01c796f4$6606b250$51f5308f@DFWFS881> Version 21 of the Reactome Knowledgebase has been released and is accessible at http://www.reactome.org. Reactome is a curated knowledgebase developed and maintained by the Reactome Knowledgebase team (Lincoln Stein's group at CSHL and Ewan Birney's group at European Bioinformatics Institute). Reactome covers human biological processes ranging from basic pathways of metabolism to complex events such as hormonal signaling and apoptosis. The information in Reactome is provided by expert bench biologists, and edited and managed as a relational database by the Reactome staff. New material is peer-reviewed and revised as necessary before publication to the web. Reactome entries are linked to corresponding ones in NCBI, Entrez Gene, RefSeq, OMIM, Ensembl genome annotations, HapMap, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO). The web interface allows users to view the curated annotations of human biological processes and orthology-based electronic inferences from these annotations for 22 other species). New topics released in Version 21 include the Rho GTPase cycle, Wnt regulation of beta-catenin, gap junction turnover, pathways for steroid hormone biosynthesis, metabolism of bile acids and bile salts and snRNP assembly. An outline of the entire influenza virus infection cycle has been completed. Updated release statistics and the Editorial Calendar are available. Reactome data can be exported in SMBL, Prot?g?, and BioPAX level 2 formats. Like everything in Reactome, these downloaded and exported materials can be reused and redistributed freely. A description of Reactome was published in March, 2007, in Genome Biology; the PDF version is available here: http://genomebiology.com/2007/8/3/r39. Reactome is seeking expert help for the curation of new modules. The Reactome knowledgebase relies on collaborations with research biologists to construct expert consensus views of key biological processes, and to integrate these with other processes already in Reactome. We are seeking new author-collaborators. If you're interested, or would like more information about our data acquisition process, please contact us at editorial at reactome.org. For questions and comments please reply to this message or write to help at reactome.org. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20070515/57dcfca3/attachment.html From zeebergb at mail.nih.gov Wed May 9 11:15:23 2007 From: zeebergb at mail.nih.gov (Barry Zeeberg) Date: Wed, 09 May 2007 14:15:23 -0400 Subject: [gofriends] a question In-Reply-To: <103235.90630.qm@web32214.mail.mud.yahoo.com> Message-ID: NCBI probably does an all against all BLAST like you need. Maybe contact the help desk at NCBI to see if they have the output files available for download. Barry On 5/9/07 1:56 PM, "Elham Khabiri" wrote: > Hello every one. > > > > I plan to work with a measure to calculate the semantic similarity between > genes or proteins and evaluate them with the sequence similarity measure like > E-value and Bit Score taken from Blast tool of those gene/protein pairs. > > > > Does any body have a set ready like the following so that I can work with > those genes and proteins to apply my measure on them? It is so difficult for > me to get the bit score and e-value for 1000-2000 gene/protein pairs using the > blast tool available online. The set that I need has the following format: > > > > Gene1 Gene2 E-value Bit score > > or > > Protein1 Protein 2 E-value Bit score > > > > > > I do appreciate it in advance. > > > > Elham > > > Ahhh...imagining that irresistible "new car" smell? > Check out new cars at Yahoo! Autos. > 3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM-> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20070509/8c990660/attachment.html From dieter.maier at biomax.com Wed May 16 02:14:31 2007 From: dieter.maier at biomax.com (Dieter Maier) Date: Wed, 16 May 2007 11:14:31 +0200 Subject: [gofriends] a question In-Reply-To: "Re: [gofriends] a question" dated May 9 References: <103235.90630.qm@web32214.mail.mud.yahoo.com> Message-ID: <17994.52087.807318.920617@pimaricin.biomax.de> MIPS (Munich information center for protein science) provides SIMAP (similarity matrix of proteins) which is an all-against-all matrix of all public protein sequences. http://mips.gsf.de/simap/ Dieter Barry Zeeberg wrote: > NCBI probably does an all against all BLAST like you need. Maybe contact the > help desk at NCBI to see if they have the output files available for > download. > > Barry > > > On 5/9/07 1:56 PM, "Elham Khabiri" wrote: > > > Hello every one. > > > > > > > > I plan to work with a measure to calculate the semantic similarity between > > genes or proteins and evaluate them with the sequence similarity measure like > > E-value and Bit Score taken from Blast tool of those gene/protein pairs. > > > > > > > > Does any body have a set ready like the following so that I can work with > > those genes and proteins to apply my measure on them? It is so difficult for > > me to get the bit score and e-value for 1000-2000 gene/protein pairs using the > > blast tool available online. The set that I need has the following format: > > > > > > > > Gene1 Gene2 E-value Bit score > > > > or > > > > Protein1 Protein 2 E-value Bit score > > > > > > > > > > > > I do appreciate it in advance. > > > > > > > > Elham > > > > > > Ahhh...imagining that irresistible "new car" smell? > > Check out new cars at Yahoo! Autos. > > > 3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM-> > > > > > Re: [gofriends] a question > > > NCBI probably does an all against all BLAST like you need. Maybe contact the help desk at NCBI to see if they have the output files available for download.
>
> Barry
>
>
> On 5/9/07 1:56 PM, "Elham Khabiri" <elhamrose at yahoo.com> wrote:
>
>
Hello every one.
>  
>
>  
> I plan to work with a measure to calculate the semantic similarity between genes or proteins and evaluate them with the sequence similarity measure like E-value and Bit Score taken from Blast tool of those gene/protein pairs.
>  
>
>  
> Does any body have a set ready like the following so that I can work with those genes and proteins to apply my measure on them? It is so difficult for me to get the bit score and e-value for 1000-2000 gene/protein pairs using the blast tool available online. The set that I need has the following format:
>  
>
>  
> Gene1      Gene2        E-value   Bit score
>  
> or
>  
> Protein1   Protein 2    E-value   Bit score
>  
>
>  
>
>  
> I do appreciate it in advance.
>  
>
>  
> Elham
>  
>
Ahhh...imagining that irresistible "new car" smell?
>  Check out new cars at Yahoo! Autos. <http://us.rd.yahoo.com/evt=48245/*http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM->
>

> > > > -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From jack at gene.concordia.ca Thu May 17 09:03:26 2007 From: jack at gene.concordia.ca (Jack Min) Date: Thu, 17 May 2007 12:03:26 -0400 (EDT) Subject: [gofriends] a question In-Reply-To: <17994.52087.807318.920617@pimaricin.biomax.de> References: <103235.90630.qm@web32214.mail.mud.yahoo.com> <17994.52087.807318.920617@pimaricin.biomax.de> Message-ID: <40973.132.205.60.212.1179417806.squirrel@gene.concordia.ca> Hi Elham, You may like to try this website - though the output is not exactly you want. https://fungalgenome.concordia.ca/tools/TargetIdentifier.html It only support blastx. However, if you have pre-run blastp, you can also use this tool to extract the information your want. Jack > > MIPS (Munich information center for protein science) provides SIMAP > (similarity matrix of proteins) which is an > all-against-all matrix of all public protein sequences. > > http://mips.gsf.de/simap/ > > Dieter > > Barry Zeeberg wrote: > >> NCBI probably does an all against all BLAST like you need. Maybe contact >> the >> help desk at NCBI to see if they have the output files available for >> download. >> >> Barry >> >> >> On 5/9/07 1:56 PM, "Elham Khabiri" wrote: >> >> > Hello every one. >> > >> > >> > >> > I plan to work with a measure to calculate the semantic similarity >> between >> > genes or proteins and evaluate them with the sequence similarity >> measure like >> > E-value and Bit Score taken from Blast tool of those gene/protein >> pairs. >> > >> > >> > >> > Does any body have a set ready like the following so that I can work >> with >> > those genes and proteins to apply my measure on them? It is so >> difficult for >> > me to get the bit score and e-value for 1000-2000 gene/protein pairs >> using the >> > blast tool available online. The set that I need has the following >> format: >> > >> > >> > >> > Gene1 Gene2 E-value Bit score >> > >> > or >> > >> > Protein1 Protein 2 E-value Bit score >> > >> > >> > >> > >> > >> > I do appreciate it in advance. >> > >> > >> > >> > Elham >> > >> > >> > Ahhh...imagining that irresistible "new car" smell? >> > Check out new cars at Yahoo! Autos. >> > > > 3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM-> >> >> >> >> >> Re: [gofriends] a question >> >> >> > STYLE='font-size:12.0px'>NCBI probably does an all against all BLAST >> like you need. Maybe contact the help desk at NCBI to see if they have >> the output files available for download.
>>
>> Barry
>>
>>
>> On 5/9/07 1:56 PM, "Elham Khabiri" <elhamrose at yahoo.com> >> wrote:
>>
>>
Hello every one.
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>I plan to work with a measure to calculate the >> semantic similarity between genes or proteins and evaluate them with the >> sequence similarity measure like E-value and Bit Score taken from Blast >> tool of those gene/protein pairs.
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>Does any body have a set ready like the >> following so that I can work with those genes and proteins to apply my >> measure on them? It is so difficult for me to get the bit score and >> e-value for 1000-2000 gene/protein pairs using the blast tool available >> online. The set that I need has the following format:
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>Gene1 >>      Gene2 >>        E-value   Bit >> score
>>  
>> > STYLE='font-size:14.0px'>or
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>Protein1   > FACE="Times New Roman">Protein 2 >>    E-value   Bit score
>>  
>> > STYLE='font-size:14.0px'>
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>I do appreciate it in advance.
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>
>> > STYLE='font-size:12.0px'>  
>> > STYLE='font-size:14.0px'>Elham
>> > STYLE='font-size:12.0px'>  
>>
Ahhh...imagining that >> irresistible "new car" smell?
>>  Check out new cars at Yahoo! Autos. > href="http://us.rd.yahoo.com/evt=48245/*http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM-"><http://us.rd.yahoo.com/evt=48245/*http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM-> >>
>>
> STYLE='font-size:12.0px'>
>> >> >> >> > > -- > This message is from the GOFriends moderated mailing list. A list of > public > announcements and discussion of the Gene Ontology (GO) project. > Problems with the list? E-mail: owner-gofriends at geneontology.org > Subscribing send "subscribe" to gofriends-request at geneontology.org > Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org > Web: http://www.geneontology.org/ > -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From sgoetz at cipf.es Fri May 18 08:16:32 2007 From: sgoetz at cipf.es (Stefan Goetz) Date: Fri, 18 May 2007 18:16:32 +0300 Subject: [gofriends] Automatic Gene Ontology Annotation Tools Message-ID: <002401c7995f$845def80$8c01230a@stefang> Hi All, we are trying to make an up-to-date list of all the working, free and public available tools who are able to generate or predict automatically (not only recover) gene ontology annotations based on (novel) sequence data. We made a first listing and would like to invite you all to discuss, complete or correct this list. Thanks in advanced for your contributions and help. Regards, Stefan Goetz Automatic Gene Ontology Annotation Tools (alphabetical order) NR: 1 Name: AutoFact Paper: BMC BioInformatics, 2005 High-throughput: yes Input Data: fasta Method: sequences are classified into 6 different annotation categories, blast-based Evidence Codes: no Manual GO curation: GO, COG, KEGG, Locus, ? GO tree visualisation: no GO graph visualisation: no Avalible: Perl implementation online Description: An Automatic Functional Annotation and Classification Tool Link: http://www.bch.umontreal.ca/Software/AutoFACT.htm NR: 2 Name: Blast2GO Paper: Bioinformatics. 2005 Sep High-throughput: yes (arround 30 000 Seqs, memory dependent) Input Data: fasta, blast-xml Method: combination of similarity search based (blast), domain based (interproscan) and datamining based (annex) annotation Annotation types: GO, InterPro, Kegg Evidence Codes: yes Manual GO curation: yes GO tree visualisation: no GO graph visualisation: yes Avalible: java web start + web service Description: A universal Gene Ontology annotation, visualization and analysis tool for functional genomics research Link: http://www.blast2go.org NR: 3 Name: GOanna/AgBase Paper: BMC Genomics High-throughput: file upload (size limit?), (user gets notified by email when data is ready) Input Data: fasta Method: Top-Blast Annotation types: GO, ? Evidence Codes: yes Manual GO curation: no GO tree visualisation: - GO graph visualisation: - Avalible: webinterface Description: GOanna is used to find annotations for proteins using similarity search. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match. Link: http://agbase.msstate.edu/GOAnna.html NR: 4 Name: GOAnno Paper: Bioinformatics. 2005 May High-throughput: one at a time Input Data: only proteins, fasta Method: evolutionary information in multible alignments organized herarchically into functional subfamilies Annotation types: GO, ? Evidence Codes: no Manual GO curation: no GO tree visualisation: - GO graph visualisation: - Avalible: webinterface Description: GO annotation based on multiple alignment Link: http://bips.u-strasbg.fr/GOAnno/ NR: 5 Name: GOblet Paper: Two NAR papers, 2003,2004 High-throughput: max ~150 seqs Input Data: fasta Method: all-hits mapping with probability scoring Annotation types: GO Evidence Codes: no Manual GO curation: no GO tree visualisation: yes GO graph visualisation: no Avalible: webinterface, output in java applet Description: A platform for Gene Ontology annotation of anonymous sequence data Link: http://goblet.molgen.mpg.de NR: 6 Name:GoFigure + GoDel Paper: Bioinformatics. 2003 Dec High-throughput: one at a time Input Data: fasta Method: GoFigure (mappping of GO terms to Blast Hits) + GODel (Selection of terms by eValue and evicdence codes) Annotation types: GO Evidence Codes: yes Manual GO curation: no GO tree visualisation: no GO graph visualisation: yes Avalible: webinterface Description: BLAST to predict Gene Ontology annotation Link: http://udgenome.ags.udel.edu/gofigure/ NR: 7 Name: GOtcha Paper: no publication High-throughput: one at a time Input Data: fasta? Method: all-hits mapping with probability scoring Annotation types: GO Evidence Codes: yes Manual GO curation: no GO tree visualisation: yes GO graph visualisation: no Avalible: webinterface Description: GOtcha uses sequence similarity searches to associate GO terms with your sequence. These are ranked by probability and displayed graphically on a subtree of Gene Ontology. You will need an up to date browser and JavaScript to get the best from the results. Link: http://www.compbio.dundee.ac.uk/gotcha/gotcha.php NR: 8 Name: HT-GO-FAT Paper: no publication High-throughput: yes Input Data: - Method: sequence similarity (custom blast db) Annotation types: GO, ? Evidence Codes: no Manual GO curation: ? GO tree visualisation: ? GO graph visualisation: ? Avalible: Windows .NET (download after request) Description: High Throughput Gene Ontology Functional Annotation Toolkit (Ht-Go-Fat) Utilized for Animal and Plant Link: http://genome4.ars.usda.gov/farm/dload.php NR: 9 Name: InterProScan Paper: Nucleic Acids Res. 2007 High-throughput: max. 10 Seqs (web interface) Input Data: fasta Method: GOs through domains Annotation types: GO, ? Evidence Codes: no Manual GO curation: no GO tree visualisation: no GO graph visualisation: no Avalible: webinterface, web service Description: Domain searches agains: BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily, SignalPHMM, TMHMM, HMMPanther, Gene3D Link: http://www.ebi.ac.uk/InterProScan/ NR: 10 Name: JAFA Paper: no publication High-throughput: one at a time Input Data: only proteins, fasta Method: Joined Assembly of Function Annotations (InterProScan, GOtcha,GoFigure, Goblet, Phydbac) Annotation types: GO Evidence Codes: yes/no Manual GO curation: no GO tree visualisation: no GO graph visualisation: no Avalible: webinterface Description: Joined Assembly of Function Annotations (InterProScan, GOtcha, GoFigure, Goblet, Phydbac) Link: http://jafa.burnham.org NR: 11 Name: OntoBlast Paper: Nucleic Acids Res. 2003 High-throughput: one at a time Input Data: only protein, fasta Method: sequence similarities Annotation types: GO Evidence Codes: no Manual GO curation: no GO tree visualisation: no GO graph visualisation: no Avalible: webinterface Description: OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms Link: http://functionalgenomics.de/ontogate/ NR: 12 CompuGen? NR: 13 GOA? NR: 13 GOAT? NR: 14 est2uni? ... -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From sorin at wayne.edu Fri May 18 09:34:49 2007 From: sorin at wayne.edu (Sorin Draghici) Date: Fri, 18 May 2007 12:34:49 -0400 Subject: [gofriends] Automatic Gene Ontology Annotation Tools In-Reply-To: <002401c7995f$845def80$8c01230a@stefang> References: <002401c7995f$845def80$8c01230a@stefang> Message-ID: <464DD5A9.1080402@wayne.edu> Stefan, Please add: Purvesh Khatri, Bogdan Done, Archana Rao, Arina Done and Sorin Draghici. A semantic analysis of the annotations of the human genome . Bioinformatics, 21(16): 3416-3421, August 2005. http://vortex.cs.wayne.edu/papers/semantic_analysis_bioinfo.pdf This is an approach to predict GO annotations based on a semantic analysis of the current GO content. There is no name as such in the paper. A tentative name could be Onto-Semantics. Regards, Sorin Stefan Goetz wrote: > Hi All, > we are trying to make an up-to-date list of all the working, free and > public available tools who are able to generate or predict automatically > (not only recover) gene ontology annotations based on (novel) sequence > data. We made a first listing and would like to invite you all to > discuss, complete or correct this list. Thanks in advanced for your > contributions and help. > Regards, > Stefan Goetz > > > Automatic Gene Ontology Annotation Tools > (alphabetical order) > > NR: 1 > Name: AutoFact > Paper: BMC BioInformatics, 2005 > High-throughput: yes > Input Data: fasta > Method: sequences are classified into 6 different annotation categories, > blast-based > Evidence Codes: no > Manual GO curation: GO, COG, KEGG, Locus, ? > GO tree visualisation: no > GO graph visualisation: no > Avalible: Perl implementation online > Description: An Automatic Functional Annotation and Classification Tool > Link: http://www.bch.umontreal.ca/Software/AutoFACT.htm > > NR: 2 > Name: Blast2GO > Paper: Bioinformatics. 2005 Sep > High-throughput: yes (arround 30 000 Seqs, memory dependent) > Input Data: fasta, blast-xml > Method: combination of similarity search based (blast), domain based > (interproscan) and datamining based (annex) annotation > Annotation types: GO, InterPro, Kegg > Evidence Codes: yes > Manual GO curation: yes > GO tree visualisation: no > GO graph visualisation: yes > Avalible: java web start + web service > Description: A universal Gene Ontology annotation, visualization and > analysis tool for functional genomics research > Link: http://www.blast2go.org > > NR: 3 > Name: GOanna/AgBase > Paper: BMC Genomics > High-throughput: file upload (size limit?), (user gets notified by email > when data is ready) > Input Data: fasta > Method: Top-Blast > Annotation types: GO, ? > Evidence Codes: yes > Manual GO curation: no > GO tree visualisation: - > GO graph visualisation: - > Avalible: webinterface > Description: GOanna is used to find annotations for proteins using > similarity search. The resulting file contains GO annotations of the top > BLAST hits. The sequence alignments are also provided so the user can > use these to access the quality of the match. > Link: http://agbase.msstate.edu/GOAnna.html > > NR: 4 > Name: GOAnno > Paper: Bioinformatics. 2005 May > High-throughput: one at a time > Input Data: only proteins, fasta > Method: evolutionary information in multible alignments organized > herarchically into functional subfamilies > Annotation types: GO, ? > Evidence Codes: no > Manual GO curation: no > GO tree visualisation: - > GO graph visualisation: - > Avalible: webinterface > Description: GO annotation based on multiple alignment > Link: http://bips.u-strasbg.fr/GOAnno/ > > NR: 5 > Name: GOblet > Paper: Two NAR papers, 2003,2004 > High-throughput: max ~150 seqs > Input Data: fasta > Method: all-hits mapping with probability scoring > Annotation types: GO > Evidence Codes: no > Manual GO curation: no > GO tree visualisation: yes > GO graph visualisation: no > Avalible: webinterface, output in java applet > Description: A platform for Gene Ontology annotation of anonymous > sequence data > Link: http://goblet.molgen.mpg.de > > NR: 6 > Name:GoFigure + GoDel > Paper: Bioinformatics. 2003 Dec > High-throughput: one at a time > Input Data: fasta > Method: GoFigure (mappping of GO terms to Blast Hits) + GODel (Selection > of terms by eValue and evicdence codes) > Annotation types: GO > Evidence Codes: yes > Manual GO curation: no > GO tree visualisation: no > GO graph visualisation: yes > Avalible: webinterface > Description: BLAST to predict Gene Ontology annotation > Link: http://udgenome.ags.udel.edu/gofigure/ > > NR: 7 > Name: GOtcha > Paper: no publication > High-throughput: one at a time > Input Data: fasta? > Method: all-hits mapping with probability scoring > Annotation types: GO > Evidence Codes: yes > Manual GO curation: no > GO tree visualisation: yes > GO graph visualisation: no > Avalible: webinterface > Description: GOtcha uses sequence similarity searches to associate GO > terms with your sequence. These are ranked by probability and displayed > graphically on a subtree of Gene Ontology. You will need an up to date > browser and JavaScript to get the best from the results. > Link: http://www.compbio.dundee.ac.uk/gotcha/gotcha.php > > NR: 8 > Name: HT-GO-FAT > Paper: no publication > High-throughput: yes > Input Data: - > Method: sequence similarity (custom blast db) > Annotation types: GO, ? > Evidence Codes: no > Manual GO curation: ? > GO tree visualisation: ? > GO graph visualisation: ? > Avalible: Windows .NET (download after request) > Description: High Throughput Gene Ontology Functional Annotation Toolkit > (Ht-Go-Fat) Utilized for Animal and Plant > Link: http://genome4.ars.usda.gov/farm/dload.php > > NR: 9 > Name: InterProScan > Paper: Nucleic Acids Res. 2007 > High-throughput: max. 10 Seqs (web interface) > Input Data: fasta > Method: GOs through domains > Annotation types: GO, ? > Evidence Codes: no > Manual GO curation: no > GO tree visualisation: no > GO graph visualisation: no > Avalible: webinterface, web service > Description: Domain searches agains: BlastProDom, FPrintScan, HMMPIR, > HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily, > SignalPHMM, TMHMM, HMMPanther, Gene3D > Link: http://www.ebi.ac.uk/InterProScan/ > > NR: 10 > Name: JAFA > Paper: no publication > High-throughput: one at a time > Input Data: only proteins, fasta > Method: Joined Assembly of Function Annotations (InterProScan, > GOtcha,GoFigure, Goblet, Phydbac) > Annotation types: GO > Evidence Codes: yes/no > Manual GO curation: no > GO tree visualisation: no > GO graph visualisation: no > Avalible: webinterface > Description: Joined Assembly of Function Annotations (InterProScan, > GOtcha, GoFigure, Goblet, Phydbac) > Link: http://jafa.burnham.org > > NR: 11 > Name: OntoBlast > Paper: Nucleic Acids Res. 2003 > High-throughput: one at a time > Input Data: only protein, fasta > Method: sequence similarities > Annotation types: GO > Evidence Codes: no > Manual GO curation: no > GO tree visualisation: no > GO graph visualisation: no > Avalible: webinterface > Description: OntoBlast function: From sequence similarities directly to > potential functional annotations by ontology terms > Link: http://functionalgenomics.de/ontogate/ > > > NR: 12 > CompuGen? > > NR: 13 > GOA? > > NR: 13 > GOAT? > > NR: 14 > est2uni? > > > ... > > > > -- > This message is from the GOFriends moderated mailing list. A list of public > announcements and discussion of the Gene Ontology (GO) project. > Problems with the list? E-mail: owner-gofriends at geneontology.org > Subscribing send "subscribe" to gofriends-request at geneontology.org > Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org > Web: http://www.geneontology.org/ > > -- Sorin Draghici, Ph.D. Director of the Bioinformatics Core, Karmanos Cancer Institute Associate Professor Tel: (313) 577-5484 Dept. of Computer Science Fax: (313) 577-6868 Wayne State University 5143 Cass Ave, Room 431 State Hall, Detroit, MI, 48202 WWW: http://vortex.cs.wayne.edu/Sorin/ (personal) WWW: http://vortex.cs.wayne.edu/Projects.html (lab) Check out my recent book: Data Analysis Tools for Microarrays: http://www.crcpress.com/shopping_cart/products/product_detail.asp?sku=C3154&parent_id=&pc= -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20070518/f038ddd2/attachment.html From jforment at ibmcp.upv.es Mon May 21 04:10:24 2007 From: jforment at ibmcp.upv.es (Javier Forment Millet) Date: Mon, 21 May 2007 13:10:24 +0200 Subject: [gofriends] Automatic Gene Ontology Annotation Tools In-Reply-To: <002401c7995f$845def80$8c01230a@stefang> References: <002401c7995f$845def80$8c01230a@stefang> Message-ID: <1179745824.46517e207366b@webmail.upv.es> Hi,... I would like to do some comments about the suggestion of including EST2uni in a list of public available tools who are able to generate or predict automatically gene ontology annotations based on sequence data. EST2uni (http://www.melogen.upv.es/genomica/web_estpipe/) is an open, parallel tool for automated EST analysis and annotation, and database creation with a data mining web interface. It is an integrated, highly-configurable EST analysis and data mining software package that completely automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections. It can be run in parallel in a PC cluster in order to reduce the time necessary to do the analysis. A web site linked to the database showing statistics on the collection, with complex queries capabilities, and tools for data mining and retrieval is also created by EST2uni. EST2uni includes a step of functional annotation of the unigenes using Gene Ontology classification, but, at the moment, it uses a simple BLAST comparison with a GO-annotated organism, taking the GO annotation of the top-BLAST hit. However, the EST2uni pipeline uses standard EST analysis tools and the software has a modular design to ease the addition of new analysis and the configuration of the existing ones, so it is easy to include any GO-annotation tool which could be used automatically in a computer pipeline. Actually, we are in the process of including BLAST2GO as a GO-annotation tool in EST2uni. Regarding this, it could be very interesting to add this feature to the table of features of the GO annotation tools that you are preparing, i.e, the ability to integrate the GO annotation tool in an automated pipeline (not only available as an stand-alone application). We think that it is a very important and desirable feature in order to be able to integrate the GO annotation tool with other analysis tools. Thanks, and keep on the good work... Javier. Mensaje citado por Stefan Goetz : > Hi All, > we are trying to make an up-to-date list of all the working, free and > public available tools who are able to generate or predict automatically > (not only recover) gene ontology annotations based on (novel) sequence > data. We made a first listing and would like to invite you all to > discuss, complete or correct this list. Thanks in advanced for your > contributions and help. > Regards, > Stefan Goetz > > > Automatic Gene Ontology Annotation Tools > (alphabetical order) > > NR: 1 > Name: AutoFact > Paper: BMC BioInformatics, 2005 > High-throughput: yes > Input Data: fasta > Method: sequences are classified into 6 different annotation categories, > blast-based > Evidence Codes: no > Manual GO curation: GO, COG, KEGG, Locus, ? > GO tree visualisation: no > GO graph visualisation: no > Avalible: Perl implementation online > Description: An Automatic Functional Annotation and Classification Tool > Link: http://www.bch.umontreal.ca/Software/AutoFACT.htm > > NR: 2 > Name: Blast2GO > Paper: Bioinformatics. 2005 Sep > High-throughput: yes (arround 30 000 Seqs, memory dependent) > Input Data: fasta, blast-xml > Method: combination of similarity search based (blast), domain based > (interproscan) and datamining based (annex) annotation > Annotation types: GO, InterPro, Kegg > Evidence Codes: yes > Manual GO curation: yes > GO tree visualisation: no > GO graph visualisation: yes > Avalible: java web start + web service > Description: A universal Gene Ontology annotation, visualization and > analysis tool for functional genomics research > Link: http://www.blast2go.org > > NR: 3 > Name: GOanna/AgBase > Paper: BMC Genomics > High-throughput: file upload (size limit?), (user gets notified by email > when data is ready) > Input Data: fasta > Method: Top-Blast > Annotation types: GO, ? > Evidence Codes: yes > Manual GO curation: no > GO tree visualisation: - > GO graph visualisation: - > Avalible: webinterface > Description: GOanna is used to find annotations for proteins using > similarity search. The resulting file contains GO annotations of the top > BLAST hits. The sequence alignments are also provided so the user can > use these to access the quality of the match. > Link: http://agbase.msstate.edu/GOAnna.html > > NR: 4 > Name: GOAnno > Paper: Bioinformatics. 2005 May > High-throughput: one at a time > Input Data: only proteins, fasta > Method: evolutionary information in multible alignments organized > herarchically into functional subfamilies > Annotation types: GO, ? > Evidence Codes: no > Manual GO curation: no > GO tree visualisation: - > GO graph visualisation: - > Avalible: webinterface > Description: GO annotation based on multiple alignment > Link: http://bips.u-strasbg.fr/GOAnno/ > > NR: 5 > Name: GOblet > Paper: Two NAR papers, 2003,2004 > High-throughput: max ~150 seqs > Input Data: fasta > Method: all-hits mapping with probability scoring > Annotation types: GO > Evidence Codes: no > Manual GO curation: no > GO tree visualisation: yes > GO graph visualisation: no > Avalible: webinterface, output in java applet > Description: A platform for Gene Ontology annotation of anonymous > sequence data > Link: http://goblet.molgen.mpg.de > > NR: 6 > Name:GoFigure + GoDel > Paper: Bioinformatics. 2003 Dec > High-throughput: one at a time > Input Data: fasta > Method: GoFigure (mappping of GO terms to Blast Hits) + GODel (Selection > of terms by eValue and evicdence codes) > Annotation types: GO > Evidence Codes: yes > Manual GO curation: no > GO tree visualisation: no > GO graph visualisation: yes > Avalible: webinterface > Description: BLAST to predict Gene Ontology annotation > Link: http://udgenome.ags.udel.edu/gofigure/ > > NR: 7 > Name: GOtcha > Paper: no publication > High-throughput: one at a time > Input Data: fasta? > Method: all-hits mapping with probability scoring > Annotation types: GO > Evidence Codes: yes > Manual GO curation: no > GO tree visualisation: yes > GO graph visualisation: no > Avalible: webinterface > Description: GOtcha uses sequence similarity searches to associate GO > terms with your sequence. These are ranked by probability and displayed > graphically on a subtree of Gene Ontology. You will need an up to date > browser and JavaScript to get the best from the results. > Link: http://www.compbio.dundee.ac.uk/gotcha/gotcha.php > > NR: 8 > Name: HT-GO-FAT > Paper: no publication > High-throughput: yes > Input Data: - > Method: sequence similarity (custom blast db) > Annotation types: GO, ? > Evidence Codes: no > Manual GO curation: ? > GO tree visualisation: ? > GO graph visualisation: ? > Avalible: Windows .NET (download after request) > Description: High Throughput Gene Ontology Functional Annotation Toolkit > (Ht-Go-Fat) Utilized for Animal and Plant > Link: http://genome4.ars.usda.gov/farm/dload.php > > NR: 9 > Name: InterProScan > Paper: Nucleic Acids Res. 2007 > High-throughput: max. 10 Seqs (web interface) > Input Data: fasta > Method: GOs through domains > Annotation types: GO, ? > Evidence Codes: no > Manual GO curation: no > GO tree visualisation: no > GO graph visualisation: no > Avalible: webinterface, web service > Description: Domain searches agains: BlastProDom, FPrintScan, HMMPIR, > HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily, > SignalPHMM, TMHMM, HMMPanther, Gene3D > Link: http://www.ebi.ac.uk/InterProScan/ > > NR: 10 > Name: JAFA > Paper: no publication > High-throughput: one at a time > Input Data: only proteins, fasta > Method: Joined Assembly of Function Annotations (InterProScan, > GOtcha,GoFigure, Goblet, Phydbac) > Annotation types: GO > Evidence Codes: yes/no > Manual GO curation: no > GO tree visualisation: no > GO graph visualisation: no > Avalible: webinterface > Description: Joined Assembly of Function Annotations (InterProScan, > GOtcha, GoFigure, Goblet, Phydbac) > Link: http://jafa.burnham.org > > NR: 11 > Name: OntoBlast > Paper: Nucleic Acids Res. 2003 > High-throughput: one at a time > Input Data: only protein, fasta > Method: sequence similarities > Annotation types: GO > Evidence Codes: no > Manual GO curation: no > GO tree visualisation: no > GO graph visualisation: no > Avalible: webinterface > Description: OntoBlast function: From sequence similarities directly to > potential functional annotations by ontology terms > Link: http://functionalgenomics.de/ontogate/ > > > NR: 12 > CompuGen? > > NR: 13 > GOA? > > NR: 13 > GOAT? > > NR: 14 > est2uni? > > > ... > > > > -- > This message is from the GOFriends moderated mailing list. A list of public > announcements and discussion of the Gene Ontology (GO) project. > Problems with the list? E-mail: owner-gofriends at geneontology.org > Subscribing send "subscribe" to gofriends-request at geneontology.org > Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org > Web: http://www.geneontology.org/ > -- 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 -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From asidhu at biomap.org Mon May 21 07:53:21 2007 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Tue, 22 May 2007 00:53:21 +1000 Subject: [gofriends] Call for Chapters: Biomedical Data and Applications by Springer Message-ID: <1179759201.4651b26141f1d@email.ixwebhosting.com> *********************************************************** Call for Book Chapters Biomedical Data and Applications http://biomed.biomap.org/ *********************************************************** Editors: Amandeep S. Sidhu, Tharam S. Dillon, Elizabeth Chang Digital Ecosystems and Business Intelligence, Curtin University of Technology, Perth, Australia Volume: Studies in Computational Intelligence Series Publisher: Springer http://www.springer.com/series/7092/ ************************************************************ Deadline: 30 June 2007 ************************************************************ Introduction: The goal of this book is to cover biomedical data and applications identifying new issues and directions for future research in biomedical domain. The book will become a useful guide for researchers, practitioners, and graduate-level students interested in learning state-of-the-art development in biomedical data management, data-intensive bioinformatics systems, and other miscellaneous biological database applications. The content of this book is at an introductory and medium technical level. ************************************************************* Topics: Chapters in the book will broadly address following areas: * Conceptual Models for Biological and Medical Data * Data Representation and Visualization * Biomedical Databases and Data Integration * Biomedical Data Analysis and Interoperability * Biological Query Processing, Query Optimization, and Information Retrieval * Biomedical Ontologies and taxonomies * Ontology-driven Biomedical Systems * Computational Methods for Microarray analysis, Protein and RNA structure prediction * Feature selection and pattern discovery in biological data * Modelling Biological Pathways * Health Care Information Systems * Electronic Health Records * Biomedical Data Privacy and Security * Clinical Assessment and Patient Diagnosis * Disease Control and Prevention * Data mining applications in bioinformatics, biomedicine, health care and other biomedical domain areas **************************************************************** Publication: The Book will be published in Studies in Computational Intelligence of Springer in Late 2007. Studies in Computational Intelligence Series publishes new developments and advances in the various areas of computational intelligence. **************************************************************** Submission Instructions: Papers should be original and should not be submitted for publication or published elsewhere. All papers are to be submitted electronically (PDF or MS word format preferred) by email to: Amandeep.Sidhu at cbs.curtin.edu.au For details on how to prepare the manuscripts and style files refer to: http://www.springer.com/west/home/new+&+forthcoming+titles+(default)?SGWID=4-40356-69-173623546-0&detailsPage=contentItemPage&contentItemId=149813&CIPageCounter=CI_FOR_AUTHORS_AND_EDITORS_PAGE1 **************************************************************** Important Dates: June 30, 2007 Last day to email a letter of intent July 31, 2007 Deadline to submit a full book chapter paper August 30, 2007 Notification of acceptance with referee comments and revision comments September 30, 2007 Deadline to submit final version of the accepted chapters **************************************************************** Editors: Amandeep S. Sidhu, Prof. Tharam S. Dillon, Prof. Elizabeth Chang Digital Ecosystems & Business Intelligence Institute, Curtin University of Technology, Australia http://debii.curtin.edu.au/ **************************************************************** -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From idoerg at gmail.com Mon May 21 08:50:00 2007 From: idoerg at gmail.com (I. Friedberg) Date: Mon, 21 May 2007 08:50:00 -0700 Subject: [gofriends] Automatic Gene Ontology Annotation Tools Message-ID: My corrections to the JAFA listing: NR: 10 > Name: JAFA > Paper: Iddo Friedberg, Tim Harder and Adam Godzik JAFA: a Protein Function Annotation Meta Server Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W379-81 > High-throughput: one at a time > Input Data: only proteins, fasta > Method: Joined Assembly of Function Annotations (InterProScan, > GOtcha,GoFigure, Goblet, Phydbac) > Annotation types: GO > Evidence Codes: yes/no > Manual GO curation: no > GO tree visualisation: YES > GO graph visualisation: YES > Available: web interface > Description: Joined Assembly of Function Annotations (InterProScan, > GOtcha, GoFigure, Goblet, Phydbac) > Link: http://jafa.burnham.org And adding PFP: > Name: PFP > Paper: Hawkins t, Luban S and Kihara D Enhanced automated function prediction using distantly related sequences and contextual association by PFP Protein Sci. 2006 Jun;15(6):1550-6 > High-throughput: one at a time > Input Data: only proteins, fasta > Method: PSI-BLAST with a Function Associated matrix > Annotation types: GO > Evidence Codes: no > Manual GO curation: no > GO tree visualisation: no > GO graph visualisation: no > Available: web interface > Description: PSI BLAST coupled with curated associateion matrices to increase sensitivity and specificity of predictions. > Link: http://dragon.bio.purdue.edu/pfp/index.html -- I. Friedberg "The only problem with troubleshooting is that sometimes trouble shoots back." -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/gofriends/attachments/20070521/95f92314/attachment.html From jane at ebi.ac.uk Fri May 25 07:43:10 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Fri, 25 May 2007 15:43:10 +0100 Subject: [gofriends] tool to visualise terms in GO tree Message-ID: <4656F5FE.8080906@ebi.ac.uk> Hello - does anyone have a tool that would be able to help this user please? thanks, Jane contactName: Kangwen Deng contactEmail: dengk at wyeth.com contactText: Suggestion needed! I applied sigPathway analysis to my microarray (rat affy 230.2.0)results and got a list of GO terms that are over-represented. What I want to do is: link all these GO terms to visulize them in a GO tree. DO you know which tool can do this? Thanks. -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From peter.robinson at charite.de Fri May 25 08:20:57 2007 From: peter.robinson at charite.de (Peter Robinson) Date: Fri, 25 May 2007 17:20:57 +0200 Subject: [gofriends] tool to visualise terms in GO tree In-Reply-To: <4656F5FE.8080906@ebi.ac.uk> References: <4656F5FE.8080906@ebi.ac.uk> Message-ID: <4656FED9.10602@charite.de> Jane Lomax wrote: > Hello - does anyone have a tool that would be able to help this user > please? > > thanks, > > Jane > > > contactName: Kangwen Deng > contactEmail: dengk at wyeth.com > contactText: Suggestion needed! > I applied sigPathway analysis to my microarray (rat affy 230.2.0)results > and got a list of GO terms that are over-represented. What I want to do > is: link all these GO terms to visulize them in a GO tree. DO you know > which tool can do this? Thanks. > The Ontologizer is a Java webstart program that creates a display of all significant terms in the GO graph as well as the anscestors of the terms. It determines significant genes based upon both the standard Fisher exact test as well as a novel method we have termed "parent-child analysis" that we have shown to reduce the number of false-positives. The Ontologizer can be started from this webpage: http://www.charite.de/ch/medgen/ontologizer/ by clicking on the webstart icon; It requires that the user has a Java runtime environment (1.5 or later). Full graphics capabilities require that the user installs graphviz on his/her system, which is relatively easy. Full instructions are provided on our webpage. Hope this helps, Peter > > -- > This message is from the GOFriends moderated mailing list. A list of > public > announcements and discussion of the Gene Ontology (GO) project. > Problems with the list? E-mail: owner-gofriends at geneontology.org > Subscribing send "subscribe" to gofriends-request at geneontology.org > Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org > Web: http://www.geneontology.org/ > -- Dr. med. Peter N. Robinson, MSc. Institut f?r Medizinische Genetik Universit?tsklinikum Charite Humboldt-Universit?t Augustenburger Platz 1 13353 Berlin Germany voice: 49-30-450569124 fax: 49-30-450569915 email: peter.robinson at charite.de http://www.charite.de/ch/medgen/robinson -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From sgoetz at cipf.es Fri May 25 07:24:21 2007 From: sgoetz at cipf.es (Stefan Goetz) Date: Fri, 25 May 2007 17:24:21 +0300 Subject: [gofriends] tool to visualise terms in GO tree In-Reply-To: <4656F5FE.8080906@ebi.ac.uk> Message-ID: <001901c79ed8$62ff6de0$8c01230a@ssssgggg> Hi Kangwen and Jane, GO visualization is one of Blast2GOs main features. Load you annotations (file->import->annotation->file.annot) like: gene1 GO:000123,GO:000124 gene2 GO:000567 ... and than generate a "Combined graph" applying filters and coloring parameters. Tree visualization is not supported since we don't think that this is a very intuitive way of exploring GO DAG hierarchy. Export the graph data and statistical graphs/pies can be generates as well. For more information the tutorial on our website (http://blast2go.bioinfo.cipf.es) may help - or write us a mail. To run Blast2GO you just need Internet and Java. Good luck! Stefan PD.: http://www.geneontology.org/GO.tools.other.shtml#blast2go Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher's Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. > -----Original Message----- > From: owner-gofriends at genome.stanford.edu > [mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Jane Lomax > Sent: Friday, May 25, 2007 5:43 PM > To: gofriends at genome.stanford.edu; GO Help List; dengk at wyeth.com > Subject: [gofriends] tool to visualise terms in GO tree > > > Hello - does anyone have a tool that would be able to help > this user please? > > thanks, > > Jane > > > contactName: Kangwen Deng > contactEmail: dengk at wyeth.com > contactText: Suggestion needed! > I applied sigPathway analysis to my microarray (rat affy > 230.2.0)results > and got a list of GO terms that are over-represented. What I > want to do > is: link all these GO terms to visulize them in a GO tree. DO > you know > which tool can do this? Thanks. > > > -- > This message is from the GOFriends moderated mailing list. A > list of public > announcements and discussion of the Gene Ontology (GO) project. > Problems with the list? E-mail: > owner-gofriends at geneontology.org > Subscribing send "subscribe" to > gofriends-request at geneontology.org > Unsubscribing send "unsubscribe" to > gofriends-request at geneontology.org > Web: http://www.geneontology.org/ > -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From jane at ebi.ac.uk Fri May 25 10:16:34 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Fri, 25 May 2007 18:16:34 +0100 Subject: [gofriends] Gene Ontology Newsletter - May issue Message-ID: <465719F2.1000102@ebi.ac.uk> Gene Ontology Newsletter May 2007, Issue No. 5 In this issue: 1. OBO-Edit 1.1 Officially Released 2. OBO-Edit tip: loading from URLs 3. Where did the ?unknown? terms go? 4. New AmiGO URLs 5. New electronic GO annotation method using gene orthology data from Ensembl 6. Public GO Database MySQL mirror now available The text of the newsletter can be viewed online or downloaded: HTML: http://www.geneontology.org/newsletter/current-newsletter.shtml PDF: http://www.geneontology.org/newsletter/current-newsletter.pdf Please contact the Gene Ontology Consortium with any comments or suggestions at gohelp at geneontology.org. Frequently asked questions may appear as tutorials or tips in upcoming newsletters. -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From steven.maere at psb.ugent.be Fri May 25 07:57:15 2007 From: steven.maere at psb.ugent.be (Steven Maere) Date: Fri, 25 May 2007 16:57:15 +0200 Subject: [gofriends] tool to visualise terms in GO tree In-Reply-To: <4656F5FE.8080906@ebi.ac.uk> References: <4656F5FE.8080906@ebi.ac.uk> Message-ID: <4656F94B.5020203@psb.ugent.be> Hi Kangwen, You can probably use BiNGO, which is a plugin for the visualization platform Cytoscape. See http://www.psb.ugent.be/cbd/papers/BiNGO/ Best, Steven Jane Lomax wrote: > Hello - does anyone have a tool that would be able to help this user > please? > > thanks, > > Jane > > > contactName: Kangwen Deng > contactEmail: dengk at wyeth.com > contactText: Suggestion needed! > I applied sigPathway analysis to my microarray (rat affy > 230.2.0)results and got a list of GO terms that are over-represented. > What I want to do is: link all these GO terms to visulize them in a GO > tree. DO you know which tool can do this? Thanks. > > > -- > This message is from the GOFriends moderated mailing list. A list of > public > announcements and discussion of the Gene Ontology (GO) project. > Problems with the list? E-mail: > owner-gofriends at geneontology.org > Subscribing send "subscribe" to > gofriends-request at geneontology.org > Unsubscribing send "unsubscribe" to > gofriends-request at geneontology.org > Web: http://www.geneontology.org/ -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group Ghent University / VIB Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3692 fax: +32 9 331 3809 email: stmae at psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ================================================================== -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/ From aconesa at cipf.es Mon May 28 01:45:24 2007 From: aconesa at cipf.es (Ana Conesa) Date: Mon, 28 May 2007 08:45:24 +0000 Subject: [gofriends] Automatic Gene Ontology Annotation Tools In-Reply-To: <000301c79f00$064f86c0$6501a8c0@ssssgggg> References: <000301c79f00$064f86c0$6501a8c0@ssssgggg> Message-ID: <465A96A4.20006@cipf.es> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Chris I think that the development of a MAIGOT or any protocol for recording metadata on GO tools is very interesting, but not only for having a standardized way to describe GO tool but specially with the idea of providing in the end a resource where people could search for tools having specific functionalities. The number and diversity of GO tools is very large already and many of them have features that go beyond to what could fit in a simple 3 category system -such as now- or which can be well described in a short description. We will love to participate in that elaboration. I also want to clarify that our question to the list on Automatic Annotation Tools was not with the aim of creating an own catalog but simply to complete "Table 1" in the manuscript we are preparing at the moment... we really do not want to maintain a listing of tools!!! Cheers, Ana Stefan Goetz wrote: > Hi Chis, > sure, I think that's a very good idea to present the tools > characteristics based on a metadata model and list of tags. Would help > to clear a lot of peoples doubts on which tool actually to use. I would > be happy to contribute in any way. > Did you think than about any kind of userfreindly search interface to > obtain, for example, what I was searching for: a lis of tools only for > automatic functional annotation? > Cheers, Stefan > > >> -----Original Message----- >> From: Chris Mungall [mailto:cjm at fruitfly.org] >> Sent: Thursday, May 24, 2007 3:47 AM >> To: sgoetz at cipf.es >> Cc: Eurie Hong; Jane Lomax; Amelia Ireland; Seth Carbon >> Subject: Re: [gofriends] Automatic Gene Ontology Annotation Tools >> >> >> Hi Stefan >> >> I don't know if you know but we maintain a list of tools here: >> http://www.geneontology.org/GO.tools.shtml >> >> as it happens we are just in the process of re-engineering this from >> a collection to web pages into metadata that can be used to generate >> nice html. >> >> we are more than happy for you to also have your own list of tools, >> but perhaps it would be easier for us and for the community if we >> collaborated on maintaining the core tool metadata. We could each >> present the metadata in our own way. We would have some protocol to >> avoid forcing people to submit one set of metadata to us and another >> to you. Would you agree? >> >> If so, then the first thing we should decide is the minimal >> information about a GO tool (MIAGOT?). This would be a simple but >> extensible list of tags, essentially the union of what you >> have below >> and the info we currently maintain. >> >> Cheers >> Chris >> >> On May 18, 2007, at 8:16 AM, Stefan Goetz wrote: >> >>> Hi All, >>> we are trying to make an up-to-date list of all the >> working, free and >>> public available tools who are able to generate or predict >>> automatically >>> (not only recover) gene ontology annotations based on (novel) >>> sequence >>> data. We made a first listing and would like to invite you all to >>> discuss, complete or correct this list. Thanks in advanced for your >>> contributions and help. >>> Regards, >>> Stefan Goetz >>> >>> >>> Automatic Gene Ontology Annotation Tools >>> (alphabetical order) >>> >>> NR: 1 >>> Name: AutoFact >>> Paper: BMC BioInformatics, 2005 >>> High-throughput: yes >>> Input Data: fasta >>> Method: sequences are classified into 6 different annotation >>> categories, >>> blast-based >>> Evidence Codes: no >>> Manual GO curation: GO, COG, KEGG, Locus, ? >>> GO tree visualisation: no >>> GO graph visualisation: no >>> Avalible: Perl implementation online >>> Description: An Automatic Functional Annotation and Classification >>> Tool >>> Link: http://www.bch.umontreal.ca/Software/AutoFACT.htm >>> >>> NR: 2 >>> Name: Blast2GO >>> Paper: Bioinformatics. 2005 Sep >>> High-throughput: yes (arround 30 000 Seqs, memory dependent) >>> Input Data: fasta, blast-xml >>> Method: combination of similarity search based (blast), domain based >>> (interproscan) and datamining based (annex) annotation >>> Annotation types: GO, InterPro, Kegg >>> Evidence Codes: yes >>> Manual GO curation: yes >>> GO tree visualisation: no >>> GO graph visualisation: yes >>> Avalible: java web start + web service >>> Description: A universal Gene Ontology annotation, visualization and >>> analysis tool for functional genomics research >>> Link: http://www.blast2go.org >>> >>> NR: 3 >>> Name: GOanna/AgBase >>> Paper: BMC Genomics >>> High-throughput: file upload (size limit?), (user gets notified by >>> email >>> when data is ready) >>> Input Data: fasta >>> Method: Top-Blast >>> Annotation types: GO, ? >>> Evidence Codes: yes >>> Manual GO curation: no >>> GO tree visualisation: - >>> GO graph visualisation: - >>> Avalible: webinterface >>> Description: GOanna is used to find annotations for proteins using >>> similarity search. The resulting file contains GO annotations of >>> the top >>> BLAST hits. The sequence alignments are also provided so >> the user can >>> use these to access the quality of the match. >>> Link: http://agbase.msstate.edu/GOAnna.html >>> >>> NR: 4 >>> Name: GOAnno >>> Paper: Bioinformatics. 2005 May >>> High-throughput: one at a time >>> Input Data: only proteins, fasta >>> Method: evolutionary information in multible alignments organized >>> herarchically into functional subfamilies >>> Annotation types: GO, ? >>> Evidence Codes: no >>> Manual GO curation: no >>> GO tree visualisation: - >>> GO graph visualisation: - >>> Avalible: webinterface >>> Description: GO annotation based on multiple alignment >>> Link: http://bips.u-strasbg.fr/GOAnno/ >>> >>> NR: 5 >>> Name: GOblet >>> Paper: Two NAR papers, 2003,2004 >>> High-throughput: max ~150 seqs >>> Input Data: fasta >>> Method: all-hits mapping with probability scoring >>> Annotation types: GO >>> Evidence Codes: no >>> Manual GO curation: no >>> GO tree visualisation: yes >>> GO graph visualisation: no >>> Avalible: webinterface, output in java applet >>> Description: A platform for Gene Ontology annotation of anonymous >>> sequence data >>> Link: http://goblet.molgen.mpg.de >>> >>> NR: 6 >>> Name:GoFigure + GoDel >>> Paper: Bioinformatics. 2003 Dec >>> High-throughput: one at a time >>> Input Data: fasta >>> Method: GoFigure (mappping of GO terms to Blast Hits) + GODel >>> (Selection >>> of terms by eValue and evicdence codes) >>> Annotation types: GO >>> Evidence Codes: yes >>> Manual GO curation: no >>> GO tree visualisation: no >>> GO graph visualisation: yes >>> Avalible: webinterface >>> Description: BLAST to predict Gene Ontology annotation >>> Link: http://udgenome.ags.udel.edu/gofigure/ >>> >>> NR: 7 >>> Name: GOtcha >>> Paper: no publication >>> High-throughput: one at a time >>> Input Data: fasta? >>> Method: all-hits mapping with probability scoring >>> Annotation types: GO >>> Evidence Codes: yes >>> Manual GO curation: no >>> GO tree visualisation: yes >>> GO graph visualisation: no >>> Avalible: webinterface >>> Description: GOtcha uses sequence similarity searches to >> associate GO >>> terms with your sequence. These are ranked by probability and >>> displayed >>> graphically on a subtree of Gene Ontology. You will need an >> up to date >>> browser and JavaScript to get the best from the results. >>> Link: http://www.compbio.dundee.ac.uk/gotcha/gotcha.php >>> >>> NR: 8 >>> Name: HT-GO-FAT >>> Paper: no publication >>> High-throughput: yes >>> Input Data: - >>> Method: sequence similarity (custom blast db) >>> Annotation types: GO, ? >>> Evidence Codes: no >>> Manual GO curation: ? >>> GO tree visualisation: ? >>> GO graph visualisation: ? >>> Avalible: Windows .NET (download after request) >>> Description: High Throughput Gene Ontology Functional Annotation >>> Toolkit >>> (Ht-Go-Fat) Utilized for Animal and Plant >>> Link: http://genome4.ars.usda.gov/farm/dload.php >>> >>> NR: 9 >>> Name: InterProScan >>> Paper: Nucleic Acids Res. 2007 >>> High-throughput: max. 10 Seqs (web interface) >>> Input Data: fasta >>> Method: GOs through domains >>> Annotation types: GO, ? >>> Evidence Codes: no >>> Manual GO curation: no >>> GO tree visualisation: no >>> GO graph visualisation: no >>> Avalible: webinterface, web service >>> Description: Domain searches agains: BlastProDom, >> FPrintScan, HMMPIR, >>> HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily, >>> SignalPHMM, TMHMM, HMMPanther, Gene3D >>> Link: http://www.ebi.ac.uk/InterProScan/ >>> >>> NR: 10 >>> Name: JAFA >>> Paper: no publication >>> High-throughput: one at a time >>> Input Data: only proteins, fasta >>> Method: Joined Assembly of Function Annotations (InterProScan, >>> GOtcha,GoFigure, Goblet, Phydbac) >>> Annotation types: GO >>> Evidence Codes: yes/no >>> Manual GO curation: no >>> GO tree visualisation: no >>> GO graph visualisation: no >>> Avalible: webinterface >>> Description: Joined Assembly of Function Annotations (InterProScan, >>> GOtcha, GoFigure, Goblet, Phydbac) >>> Link: http://jafa.burnham.org >>> >>> NR: 11 >>> Name: OntoBlast >>> Paper: Nucleic Acids Res. 2003 >>> High-throughput: one at a time >>> Input Data: only protein, fasta >>> Method: sequence similarities >>> Annotation types: GO >>> Evidence Codes: no >>> Manual GO curation: no >>> GO tree visualisation: no >>> GO graph visualisation: no >>> Avalible: webinterface >>> Description: OntoBlast function: From sequence similarities >>> directly to >>> potential functional annotations by ontology terms >>> Link: http://functionalgenomics.de/ontogate/ >>> >>> >>> NR: 12 >>> CompuGen? >>> >>> NR: 13 >>> GOA? >>> >>> NR: 13 >>> GOAT? >>> >>> NR: 14 >>> est2uni? >>> >>> >>> ... >>> >>> >>> >>> -- >>> This message is from the GOFriends moderated mailing list. A list >>> of public >>> announcements and discussion of the Gene Ontology (GO) project. >>> Problems with the list? E-mail: owner- >>> gofriends at geneontology.org >>> Subscribing send "subscribe" to gofriends- >>> request at geneontology.org >>> Unsubscribing send "unsubscribe" to gofriends- >>> request at geneontology.org >>> Web: http://www.geneontology.org/ >>> -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGWpakvYhZZsDwY1YRAtVTAJ4nkHmBSYLjXSGWHMALL4v58R5qKACfS8yp ezfuu5DJH5yDSEt2vZ062Ew= =pdd4 -----END PGP SIGNATURE----- -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/