Ensembl 2005

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.

Damian Smedley | Ewan Birney | Javier Herrero | Graham Cameron | James G. R. Gilbert | Xosé M. Fernández-Suárez | Tim J. P. Hubbard | Thomas A. Down | Tony Cox | Richard Durbin | Simon White | Stephen Keenan | Vivek Iyer | William Spooner | Andreas Kähäri | James A. Smith | Michael Schuster | Mario Cáccamo | Arek Kasprzyk | Jessica Severin | Kevin L. Howe | Jim Stalker | Simon C. Potter | Mark Rae | Arne Stabenau | Laura Clarke | Felix Kokocinski | Jan Vogel | Stephen M. J. Searle | Kerstin Jekosch | Patrick Meidl | R. Storey | Stephen J. Trevanion | Abel Ureta-Vidal | Michele E. Clamp | Graham P. McVicker | Guy Coates | Val Curwen | Tim Cutts | Martin Hammond | H. Hotz | Damian Keefe | Craig Melsopp | Cara Woodwark | D. Andrews | Yuan Chen | Fiona Cunningham | D. London | Ian Longden | Glenn Proctor | Daniel Rios | Guy Slater | R. Durbin | E. Birney | F. Kokocinski | S. Searle | T. Hubbard | Cara Woodwark | D. Smedley | S. Potter | T. Down | M. Clamp | Damian Keefe | J. Gilbert | Yuan Chen | G. Slater | A. Kasprzyk | D. London | W. Spooner | Craig Melsopp | M. Hammond | Tony Cox | M. Cáccamo | L. Clarke | Guy Coates | T. Cutts | K. Howe | Andreas Kähäri | I. Longden | Patrick Meidl | Daniel Rios | Michael Schuster | S. Trevanion | J. Vogel | S. White | V. Curwen | X. M. Fernández-Suárez | Javier Herrero | G. Proctor | James A. Smith | A. Ureta-Vidal | S. Keenan | Arne Stabenau | R. Storey | Graham P. McVicker | J. Severin | J. Stalker | H. Hotz | V. Iyer | G. Cameron | K. Jekosch | Mark Rae | D. Andrews | P. Meidl | Fiona Cunningham | Ian Longden | G. McVicker | Laura Clarke | Simon C. Potter | Jessica Severin

[1]  Damian Smedley,et al.  Ensembl 2004 , 2004, Nucleic Acids Res..

[2]  S. Searle,et al.  The Ensembl analysis pipeline. , 2004, Genome research.

[3]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence Project: update and current status , 2003, Nucleic Acids Res..

[4]  Antony V. Cox,et al.  The Ensembl Web site: mechanics of a genome browser. , 2004, Genome research.

[5]  E. Birney,et al.  EnsMart: a generic system for fast and flexible access to biological data. , 2003, Genome research.

[6]  E. Birney,et al.  Apollo: a sequence annotation editor , 2002, Genome Biology.

[7]  R. Durbin,et al.  The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics , 2003, PLoS biology.

[8]  Simon C. Potter,et al.  An overview of Ensembl. , 2004, Genome research.

[9]  Eduardo Eyras,et al.  ESTGenes: alternative splicing from ESTs in Ensembl. , 2004, Genome research.

[10]  Alex Bateman,et al.  The InterPro Database, 2003 brings increased coverage and new features , 2003, Nucleic Acids Res..

[11]  Sean R. Eddy,et al.  The Distributed Annotation System , 2001, BMC Bioinformatics.

[12]  J. Bonfield,et al.  Finishing the euchromatic sequence of the human genome , 2004, Nature.

[13]  The FlyBase database of the Drosophila genome projects and community literature. , 2003, Nucleic acids research.

[14]  S Beck,et al.  Epigenomics: genome-wide study of methylation phenomena. , 2002, Current issues in molecular biology.

[15]  Vivek Iyer,et al.  The otter annotation system. , 2004, Genome research.

[16]  Kimberly Van Auken,et al.  WormBase: a multi-species resource for nematode biology and genomics , 2004, Nucleic Acids Res..

[17]  T. Andrews,et al.  The Ensembl automatic gene annotation system. , 2004, Genome research.

[18]  Terrence S. Furey,et al.  The UCSC Genome Browser Database , 2003, Nucleic Acids Res..

[19]  J. Ashurst,et al.  Gene annotation: prediction and testing. , 2003, Annual review of genomics and human genetics.

[20]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.

[21]  Mark Rae,et al.  The Ensembl computing architecture. , 2004, Genome research.

[22]  Matthew R. Pocock,et al.  BioJava: open source components for bioinformatics , 2000, SIGB.

[23]  International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome , 2004 .

[24]  D. Haussler,et al.  Human-mouse alignments with BLASTZ. , 2003, Genome research.

[25]  R. Durbin,et al.  GeneWise and Genomewise. , 2004, Genome research.

[26]  Rolf Apweiler,et al.  UniProt archive , 2004, Bioinform..

[27]  Lisa M. D'Souza,et al.  Genome sequence of the Brown Norway rat yields insights into mammalian evolution , 2004, Nature.

[28]  E. Birney,et al.  The Ensembl core software libraries. , 2004, Genome research.