Literature DB >> 16859520

yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.

Matthew D Wilkerson1, Shannon D Schlueter, Volker Brendel.   

Abstract

Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the acceptance of annotations into published gene sets. yrGATE is designed to facilitate rapid and accurate annotation of emerging genomes as well as to confirm, refine, or correct currently published annotations. yrGATE is highly portable and supports different standard input and output formats. The yrGATE software and usage cases are available at http://www.plantgdb.org/prj/yrGATE.

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Year:  2006        PMID: 16859520      PMCID: PMC1779557          DOI: 10.1186/gb-2006-7-7-r58

Source DB:  PubMed          Journal:  Genome Biol        ISSN: 1474-7596            Impact factor:   13.583


  32 in total

1.  Open annotation offers a democratic solution to genome sequencing.

Authors:  T Hubbard; E Birney
Journal:  Nature       Date:  2000-02-24       Impact factor: 49.962

2.  Integrating genomic homology into gene structure prediction.

Authors:  I Korf; P Flicek; D Duan; M R Brent
Journal:  Bioinformatics       Date:  2001       Impact factor: 6.937

Review 3.  Genome annotation: from sequence to biology.

Authors:  L Stein
Journal:  Nat Rev Genet       Date:  2001-07       Impact factor: 53.242

4.  The Ensembl genome database project.

Authors:  T Hubbard; D Barker; E Birney; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; L Huminiecki; A Kasprzyk; H Lehvaslaiho; P Lijnzaad; C Melsopp; E Mongin; R Pettett; M Pocock; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; M Clamp
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  Genomewide comparative analysis of alternative splicing in plants.

Authors:  Bing-Bing Wang; Volker Brendel
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-21       Impact factor: 11.205

6.  Comparative gene prediction in human and mouse.

Authors:  Genís Parra; Pankaj Agarwal; Josep F Abril; Thomas Wiehe; James W Fickett; Roderic Guigó
Journal:  Genome Res       Date:  2003-01       Impact factor: 9.043

7.  The UCSC Genome Browser Database.

Authors:  D Karolchik; R Baertsch; M Diekhans; T S Furey; A Hinrichs; Y T Lu; K M Roskin; M Schwartz; C W Sugnet; D J Thomas; R J Weber; D Haussler; W J Kent
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

8.  GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.

Authors:  Kevin L Howe; Tom Chothia; Richard Durbin
Journal:  Genome Res       Date:  2002-09       Impact factor: 9.043

9.  ASAP, a systematic annotation package for community analysis of genomes.

Authors:  Jeremy D Glasner; Paul Liss; Guy Plunkett; Aaron Darling; Tejasvini Prasad; Michael Rusch; Alexis Byrnes; Michael Gilson; Bryan Biehl; Frederick R Blattner; Nicole T Perna
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

Review 10.  Apollo: a sequence annotation editor.

Authors:  S E Lewis; S M J Searle; N Harris; M Gibson; V Lyer; J Richter; C Wiel; L Bayraktaroglu; E Birney; M A Crosby; J S Kaminker; B B Matthews; S E Prochnik; C D Smithy; J L Tupy; G M Rubin; S Misra; C J Mungall; M E Clamp
Journal:  Genome Biol       Date:  2002-12-23       Impact factor: 13.583

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  13 in total

1.  Manual curation is not sufficient for annotation of genomic databases.

Authors:  William A Baumgartner; K Bretonnel Cohen; Lynne M Fox; George Acquaah-Mensah; Lawrence Hunter
Journal:  Bioinformatics       Date:  2007-07-01       Impact factor: 6.937

2.  ORCAE: online resource for community annotation of eukaryotes.

Authors:  Lieven Sterck; Kenny Billiau; Thomas Abeel; Pierre Rouzé; Yves Van de Peer
Journal:  Nat Methods       Date:  2012-11       Impact factor: 28.547

3.  xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.

Authors:  Jon Duvick; Daniel S Standage; Nirav Merchant; Volker P Brendel
Journal:  Plant Cell       Date:  2016-03-28       Impact factor: 11.277

4.  MaizeGDB becomes 'sequence-centric'.

Authors:  Taner Z Sen; Carson M Andorf; Mary L Schaeffer; Lisa C Harper; Michael E Sparks; Jon Duvick; Volker P Brendel; Ethalinda Cannon; Darwin A Campbell; Carolyn J Lawrence
Journal:  Database (Oxford)       Date:  2009-12-07       Impact factor: 3.451

5.  MaizeGDB: curation and outreach go hand-in-hand.

Authors:  Mary L Schaeffer; Lisa C Harper; Jack M Gardiner; Carson M Andorf; Darwin A Campbell; Ethalinda K S Cannon; Taner Z Sen; Carolyn J Lawrence
Journal:  Database (Oxford)       Date:  2011-05-29       Impact factor: 3.451

6.  Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize.

Authors:  James C Schnable; Michael Freeling
Journal:  PLoS One       Date:  2011-03-10       Impact factor: 3.240

7.  xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features.

Authors:  Shannon D Schlueter; Matthew D Wilkerson; Qunfeng Dong; Volker Brendel
Journal:  Genome Biol       Date:  2006       Impact factor: 13.583

8.  PlantGDB: a resource for comparative plant genomics.

Authors:  Jon Duvick; Ann Fu; Usha Muppirala; Mukul Sabharwal; Matthew D Wilkerson; Carolyn J Lawrence; Carol Lushbough; Volker Brendel
Journal:  Nucleic Acids Res       Date:  2007-12-06       Impact factor: 16.971

9.  EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome.

Authors:  Françoise Thibaud-Nissen; Matthew Campbell; John P Hamilton; Wei Zhu; C Robin Buell
Journal:  BMC Genomics       Date:  2007-10-25       Impact factor: 3.969

10.  Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing.

Authors:  Jessica A Schlueter; Jer-Young Lin; Shannon D Schlueter; Iryna F Vasylenko-Sanders; Shweta Deshpande; Jing Yi; Majesta O'Bleness; Bruce A Roe; Rex T Nelson; Brian E Scheffler; Scott A Jackson; Randy C Shoemaker
Journal:  BMC Genomics       Date:  2007-09-19       Impact factor: 3.969

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