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Literature DB >> 12537570

An integrated computational pipeline and database to support whole-genome sequence annotation.

C J Mungall¹, S Misra, B P Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, J S Kaminker, S E Prochnik, C D Smith, E Smith, J L Tupy, C Wiel, G M Rubin, S E Lewis.

Abstract

We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome annotation. The key contributions to overall annotation quality are the marshalling of high-quality sequences for alignments and the design of a system with an adaptable and expandable flexible architecture.

Entities: Chemical Disease Gene Species

Mesh：

Year: 2002 PMID： 12537570 PMCID： PMC151183 DOI： 10.1186/gb-2002-3-12-research0081

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

28 in total

1. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors: M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal: Nat Genet Date: 2000-05 Impact factor: 38.330

2. Trans-splicing as a novel mechanism to explain interallelic complementation in Drosophila.

Authors: Fabien Mongelard; Mariano Labrador; Ellen M Baxter; Tatiana I Gerasimova; Victor G Corces
Journal: Genetics Date: 2002-04 Impact factor: 4.562

3. InterProScan--an integration platform for the signature-recognition methods in InterPro.

Authors: E M Zdobnov; R Apweiler
Journal: Bioinformatics Date: 2001-09 Impact factor: 6.937

4. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays.

Authors: E De Gregorio; P T Spellman; G M Rubin; B Lemaitre
Journal: Proc Natl Acad Sci U S A Date: 2001-10-16 Impact factor: 11.205

5. The human genome browser at UCSC.

Authors: W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal: Genome Res Date: 2002-06 Impact factor: 9.043

6. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

Authors: A Bairoch; R Apweiler
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

7. DNA Data Bank of Japan (DDBJ) for genome scale research in life science.

Authors: Y Tateno; T Imanishi; S Miyazaki; K Fukami-Kobayashi; N Saitou; H Sugawara; T Gojobori
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

8. The FlyBase database of the Drosophila genome projects and community literature.

Authors:
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

9. A computer program for aligning a cDNA sequence with a genomic DNA sequence.

Authors: L Florea; G Hartzell; Z Zhang; G M Rubin; W Miller
Journal: Genome Res Date: 1998-09 Impact factor: 9.043

10. Genie--gene finding in Drosophila melanogaster.

Authors: M G Reese; D Kulp; H Tammana; D Haussler
Journal: Genome Res Date: 2000-04 Impact factor: 9.043

29 in total

1. Biopipe: a flexible framework for protocol-based bioinformatics analysis.

Authors: Shawn Hoon; Kiran Kumar Ratnapu; Jer-Ming Chia; Balamurugan Kumarasamy; Xiao Juguang; Michele Clamp; Arne Stabenau; Simon Potter; Laura Clarke; Elia Stupka
Journal: Genome Res Date: 2003-07-17 Impact factor: 9.043

2. The Ensembl analysis pipeline.

Authors: Simon C Potter; Laura Clarke; Val Curwen; Stephen Keenan; Emmanuel Mongin; Stephen M J Searle; Arne Stabenau; Roy Storey; Michele Clamp
Journal: Genome Res Date: 2004-05 Impact factor: 9.043

Review 3. The Ensembl core software libraries.

Authors: Arne Stabenau; Graham McVicker; Craig Melsopp; Glenn Proctor; Michele Clamp; Ewan Birney
Journal: Genome Res Date: 2004-05 Impact factor: 9.043

Review 4. An overview of Ensembl.

Authors: Ewan Birney; T Daniel Andrews; Paul Bevan; Mario Caccamo; Yuan Chen; Laura Clarke; Guy Coates; James Cuff; Val Curwen; Tim Cutts; Thomas Down; Eduardo Eyras; Xose M Fernandez-Suarez; Paul Gane; Brian Gibbins; James Gilbert; Martin Hammond; Hans-Rudolf Hotz; Vivek Iyer; Kerstin Jekosch; Andreas Kahari; Arek Kasprzyk; Damian Keefe; Stephen Keenan; Heikki Lehvaslaiho; Graham McVicker; Craig Melsopp; Patrick Meidl; Emmanuel Mongin; Roger Pettett; Simon Potter; Glenn Proctor; Mark Rae; Steve Searle; Guy Slater; Damian Smedley; James Smith; Will Spooner; Arne Stabenau; James Stalker; Roy Storey; Abel Ureta-Vidal; K Cara Woodwark; Graham Cameron; Richard Durbin; Anthony Cox; Tim Hubbard; Michele Clamp
Journal: Genome Res Date: 2004-04-12 Impact factor: 9.043

Review 5. A beginner's guide to eukaryotic genome annotation.

Authors: Mark Yandell; Daniel Ence
Journal: Nat Rev Genet Date: 2012-04-18 Impact factor: 53.242

6. A Java-based fMRI processing pipeline evaluation system for assessment of univariate general linear model and multivariate canonical variate analysis-based pipelines.

Authors: Jing Zhang; Lichen Liang; Jon R Anderson; Lael Gatewood; David A Rottenberg; Stephen C Strother
Journal: Neuroinformatics Date: 2008-05-28

7. 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

8. A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome.

Authors: Mark Yandell; Adina M Bailey; Sima Misra; ShengQiang Shu; Colin Wiel; Martha Evans-Holm; Susan E Celniker; Gerald M Rubin
Journal: Proc Natl Acad Sci U S A Date: 2005-01-24 Impact factor: 11.205

9. Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster.

Authors: Jonathan L Tupy; Adina M Bailey; Gina Dailey; Martha Evans-Holm; Christian W Siebel; Sima Misra; Susan E Celniker; Gerald M Rubin
Journal: Proc Natl Acad Sci U S A Date: 2005-04-04 Impact factor: 11.205

10. Predicting DNA-binding specificities of eukaryotic transcription factors.

Authors: Adrian Schröder; Johannes Eichner; Jochen Supper; Jonas Eichner; Dierk Wanke; Carsten Henneges; Andreas Zell
Journal: PLoS One Date: 2010-11-30 Impact factor: 3.240