GOblet: a platform for Gene Ontology annotation of anonymous sequence data
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TLDR
GOblet is a comprehensive web server application providing the annotation of anonymous sequence data with Gene Ontology (GO) terms and provides an improved display of results with the aid of Java applets.Abstract:
GOblet is a comprehensive web server application providing the annotation of anonymous sequence data with Gene Ontology (GO) terms. It uses a variety of different protein databases (human, murines, invertebrates, plants, sp-trembl) and their respective GO mappings. The user selects the appropriate database and alignment threshold and thereafter submits single or multiple nucleotide or protein sequences. Results are shown in different ways, e.g. as survey statistics for the main GO categories for all sequences or as detailed results for each single sequence that has been submitted. In its newest version, GOblet allows the batch submission of sequences and provides an improved display of results with the aid of Java applets. All output data, together with the Java applet, are packed to a downloadable archive for local installation and analysis. GOblet can be accessed freely at http://goblet.molgen.mpg.de.read more
Citations
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Journal ArticleDOI
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
TL;DR: Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available, is presented.
Journal ArticleDOI
High-throughput functional annotation and data mining with the Blast2GO suite.
Stefan Götz,Juan M. García-Gómez,Javier Terol,Tim D. Williams,Shivashankar H. Nagaraj,María José Nueda,Montserrat Robles,Manuel Talon,Joaquín Dopazo,Ana Conesa +9 more
TL;DR: The Blast2GO framework is used to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.
Journal ArticleDOI
WEGO: a web tool for plotting GO annotations
Jia Ye,Lin Fang,Hongkun Zheng,Yong Zhang,Jie Chen,Zengjin Zhang,Jing Wang,Shengting Li,Ruiqiang Li,Lars Bolund,Jun Wang +10 more
TL;DR: WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results, designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of Go annotation results.
Journal ArticleDOI
Blast2GO: A comprehensive suite for functional analysis in plant genomics.
Ana Conesa,Stefan Götz +1 more
TL;DR: The Blast2GO suite is described as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary.
Journal ArticleDOI
Automated protein function prediction—the genomic challenge
TL;DR: The history of automated protein function prediction, a need for a functional annotation which is standardized and machine readable so that function prediction programs could be incorporated into larger workflows, and the latest innovations in all three topics are surveyed.
References
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M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
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Midori A. Harris,Jennifer I. Clark,Ireland A,Jane Lomax,Michael Ashburner,Michael Ashburner,R. Foulger,R. Foulger,Karen Eilbeck,Karen Eilbeck,Suzanna E. Lewis,Suzanna E. Lewis,B. Marshall,B. Marshall,Christopher J. Mungall,Christopher J. Mungall,J. Richter,J. Richter,Gerald M. Rubin,Gerald M. Rubin,Judith A. Blake,Carol J. Bult,Dolan M,Drabkin H,Janan T. Eppig,Hill Dp,L. Ni,Ringwald M,Rama Balakrishnan,Rama Balakrishnan,J. M. Cherry,J. M. Cherry,Karen R. Christie,Karen R. Christie,Maria C. Costanzo,Maria C. Costanzo,Selina S. Dwight,Selina S. Dwight,Stacia R. Engel,Stacia R. Engel,Dianna G. Fisk,Dianna G. Fisk,Jodi E. Hirschman,Jodi E. Hirschman,Eurie L. Hong,Eurie L. Hong,Robert S. Nash,Robert S. Nash,Anand Sethuraman,Anand Sethuraman,Chandra L. Theesfeld,Chandra L. Theesfeld,David Botstein,David Botstein,Kara Dolinski,Kara Dolinski,Becket Feierbach,Becket Feierbach,Tanya Z. Berardini,Tanya Z. Berardini,S. Mundodi,S. Mundodi,Seung Y. Rhee,Seung Y. Rhee,Rolf Apweiler,Daniel Barrell,Camon E,E. Dimmer,Lee,Rex L. Chisholm,Pascale Gaudet,Pascale Gaudet,Warren A. Kibbe,Warren A. Kibbe,Ranjana Kishore,Ranjana Kishore,Erich M. Schwarz,Erich M. Schwarz,Paul W. Sternberg,Paul W. Sternberg,M. Gwinn,Hannick L,Wortman J,Matthew Berriman,Matthew Berriman,Wood,Wood,de la Cruz N,de la Cruz N,Peter J. Tonellato,Peter J. Tonellato,Pankaj Jaiswal,Pankaj Jaiswal,Seigfried T,Seigfried T,White R,White R +96 more
TL;DR: The Gene Ontology (GO) project as discussed by the authors provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences.
Journal ArticleDOI
MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
Scott W. Doniger,Nathan Salomonis,Kam D. Dahlquist,Karen Vranizan,Karen Vranizan,Steven C. Lawlor,Bruce R. Conklin +6 more
TL;DR: GenMAPPFinder allows the user to rapidly identify GO terms with over-represented numbers of gene-expression changes, and generates GenMAPP graphical files where gene relationships can be explored, annotated, and files can be freely exchanged.
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