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The Ensembl project is based at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). It provides one of the most comprehensive and integrated resources of genomic data, which can be accessed through the web (www.ensembl.org) and through BioMart, FTP, Perl APIs, REST API and MySQL queries.


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How to cite this record FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: Aug. 22, 2018, 11:31 a.m.; Last accessed: Sep 20 2018 8:54 p.m.


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Record updated: Aug. 6, 2018, 9:43 a.m. by The FAIRsharing Team.

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Access / Retrieve Data


Publications

The Ensembl genome database project.

Hubbard T,Barker D,Birney E,Cameron G,Chen Y,Clark L,Cox T,Cuff J,Curwen V,Down T,Durbin R,Eyras E,Gilbert J,Hammond M,Huminiecki L,Kasprzyk A,Lehvaslaiho H,Lijnzaad P,Melsopp C,Mongin E,Pettett R,Pocock M,Potter S,Rust A,Schmidt E,Searle S,Slater G,Smith J,Spooner W,Stabenau A,Stalker J,Stupka E,Ureta-Vidal A,Vastrik I,Clamp M
Nucleic Acids Res 2001

View Paper (PubMed)

The Ensembl REST API: Ensembl Data for Any Language.

Yates A,Beal K,Keenan S,McLaren W,Pignatelli M,Ritchie GR,Ruffier M,Taylor K,Vullo A,Flicek P
Bioinformatics 2014

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The Ensembl Variant Effect Predictor.

McLaren W,Gil L,Hunt SE,Riat HS,Ritchie GR,Thormann A,Flicek P,Cunningham F
Genome Biol 2016

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Incorporating RNA-seq data into the zebrafish Ensembl genebuild.

Collins JE,White S,Searle SM,Stemple DL
Genome Res 2012

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Ensembl comparative genomics resources.

Herrero J,Muffato M,Beal K,Fitzgerald S,Gordon L,Pignatelli M,Vilella AJ,Searle SM,Amode R,Brent S,Spooner W,Kulesha E,Yates A,Flicek P
Database (Oxford) 2016

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The Ensembl Web site: mechanics of a genome browser.

Stalker J,Gibbins B,Meidl P,Smith J,Spooner W,Hotz HR,Cox AV
Genome Res 2004

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The Ensembl core software libraries.

Stabenau A,McVicker G,Melsopp C,Proctor G,Clamp M,Birney E
Genome Res 2004

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GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow J,Frankish A,Gonzalez JM,Tapanari E,Diekhans M,Kokocinski F,Aken BL,Barrell D,Zadissa A,Searle S,Barnes I,Bignell A,Boychenko V,Hunt T,Kay M,Mukherjee G,Rajan J,Despacio-Reyes G,Saunders G,Steward C,Harte R,Lin M,Howald C,Tanzer A,Derrien T,Chrast J,Walters N,Balasubramanian S,Pei B,Tress M,Rodriguez JM,Ezkurdia I,van Baren J,Brent M,Haussler D,Kellis M,Valencia A,Reymond A,Gerstein M,Guigo R,Hubbard TJ
Genome Res 2012

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Disease and phenotype data at Ensembl.

Spudich GM,Fernandez-Suarez XM
Curr Protoc Hum Genet 2011

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Genome information resources - developments at Ensembl.

Hammond MP,Birney E
Trends Genet 2004

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Ensembl BioMarts: a hub for data retrieval across taxonomic space.

Kinsella RJ,Kahari A,Haider S,Zamora J,Proctor G,Spudich G,Almeida-King J,Staines D,Derwent P,Kerhornou A,Kersey P,Flicek P
Database (Oxford) 2011

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Ensembl 2015

Cunningham F et al.
Nucleic Acids Res. 2015

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Ensembl 2007.

Hubbard TJ,Aken BL,Beal K,Ballester B,Caccamo M,Chen Y,Clarke L,Coates G,Cunningham F,Cutts T,Down T,Dyer SC,Fitzgerald S,Fernandez-Banet J,Graf S,Haider S,Hammond M,Herrero J,Holland R,Howe K,Howe K,Johnson N,Kahari A,Keefe D,Kokocinski F,Kulesha E,Lawson D,Longden I,Melsopp C,Megy K,Meidl P,Ouverdin B,Parker A,Prlic A,Rice S,Rios D,Schuster M,Sealy I,Severin J,Slater G,Smedley D,Spudich G,Trevanion S,Vilella A,Vogel J,White S,Wood M,Cox T,Curwen V,Durbin R,Fernandez-Suarez XM,Flicek P,Kasprzyk A,Proctor G,Searle S,Smith J,Ureta-Vidal A,Birney E
Nucleic Acids Res 2006

View Paper (PubMed) View Publication

Ensembl 2006.

Birney E,Andrews D,Caccamo M,Chen Y,Clarke L,Coates G,Cox T,Cunningham F,Curwen V,Cutts T,Down T,Durbin R,Fernandez-Suarez XM,Flicek P,Graf S,Hammond M,Herrero J,Howe K,Iyer V,Jekosch K,Kahari A,Kasprzyk A,Keefe D,Kokocinski F,Kulesha E,London D,Longden I,Melsopp C,Meidl P,Overduin B,Parker A,Proctor G,Prlic A,Rae M,Rios D,Redmond S,Schuster M,Sealy I,Searle S,Severin J,Slater G,Smedley D,Smith J,Stabenau A,Stalker J,Trevanion S,Ureta-Vidal A,Vogel J,White S,Woodwark C,Hubbard TJ
Nucleic Acids Res 2005

View Paper (PubMed) View Publication

The Ensembl REST API: Ensembl Data for Any Language.

Yates A,Beal K,Keenan S,McLaren W,Pignatelli M,Ritchie GR,Ruffier M,Taylor K,Vullo A,Flicek P
Bioinformatics 2014

View Paper (PubMed) View Publication

The Ensembl gene annotation system.

Aken BL,Ayling S,Barrell D,Clarke L,Curwen V,Fairley S,Fernandez Banet J,Billis K,Garcia Giron C,Hourlier T,Howe K,Kahari A,Kokocinski F,Martin FJ,Murphy DN,Nag R,Ruffier M,Schuster M,Tang YA,Vogel JH,White S,Zadissa A,Flicek P,Searle SM
Database (Oxford) 2016

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Ensembl 2014.

Flicek P,Amode MR,Barrell D,Beal K,Billis K,Brent S,Carvalho-Silva D,Clapham P,Coates G,Fitzgerald S,Gil L,Giron CG,Gordon L,Hourlier T,Hunt S,Johnson N,Juettemann T,Kahari AK,Keenan S,Kulesha E,Martin FJ,Maurel T,McLaren WM,Murphy DN,Nag R,Overduin B,Pignatelli M,Pritchard B,Pritchard E,Riat HS,Ruffier M,Sheppard D,Taylor K,Thormann A,Trevanion SJ,Vullo A,Wilder SP,Wilson M,Zadissa A,Aken BL,Birney E,Cunningham F,Harrow J,Herrero J,Hubbard TJ,Kinsella R,Muffato M,Parker A,Spudich G,Yates A,Zerbino DR,Searle SM
Nucleic Acids Res 2013

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Ensembl 2006.

Birney E,Andrews D,Caccamo M,Chen Y,Clarke L,Coates G,Cox T,Cunningham F,Curwen V,Cutts T,Down T,Durbin R,Fernandez-Suarez XM,Flicek P,Graf S,Hammond M,Herrero J,Howe K,Iyer V,Jekosch K,Kahari A,Kasprzyk A,Keefe D,Kokocinski F,Kulesha E,London D,Longden I,Melsopp C,Meidl P,Overduin B,Parker A,Proctor G,Prlic A,Rae M,Rios D,Redmond S,Schuster M,Sealy I,Searle S,Severin J,Slater G,Smedley D,Smith J,Stabenau A,Stalker J,Trevanion S,Ureta-Vidal A,Vogel J,White S,Woodwark C,Hubbard TJ
Nucleic Acids Res 2005

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ncRNA orthologies in the vertebrate lineage.

Pignatelli M,Vilella AJ,Muffato M,Gordon L,White S,Flicek P,Herrero J
Database (Oxford) 2016

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Ensembl comparative genomics resources.

Herrero J,Muffato M,Beal K,Fitzgerald S,Gordon L,Pignatelli M,Vilella AJ,Searle SM,Amode R,Brent S,Spooner W,Kulesha E,Yates A,Flicek P
Database (Oxford) 2016

View Paper (PubMed) View Publication

The Ensembl computing architecture.

Cuff JA,Coates GM,Cutts TJ,Rae M
Genome Res 2004

View Paper (PubMed) View Publication

Ensembl 2005.

Hubbard T,Andrews D,Caccamo M,Cameron G,Chen Y,Clamp M,Clarke L,Coates G,Cox T,Cunningham F,Curwen V,Cutts T,Down T,Durbin R,Fernandez-Suarez XM,Gilbert J,Hammond M,Herrero J,Hotz H,Howe K,Iyer V,Jekosch K,Kahari A,Kasprzyk A,Keefe D,Keenan S,Kokocinsci F,London D,Longden I,McVicker G,Melsopp C,Meidl P,Potter S,Proctor G,Rae M,Rios D,Schuster M,Searle S,Severin J,Slater G,Smedley D,Smith J,Spooner W,Stabenau A,Stalker J,Storey R,Trevanion S,Ureta-Vidal A,Vogel J,White S,Woodwark C,Birney E
Nucleic Acids Res 2004

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ESTGenes: alternative splicing from ESTs in Ensembl.

Eyras E,Caccamo M,Curwen V,Clamp M
Genome Res 2004

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WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.

Zerbino DR,Johnson N,Juettemann T,Wilder SP,Flicek P
Bioinformatics 2013

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Ensembl 2017.

Aken BL,Achuthan P,Akanni W,Amode MR,Bernsdorff F,Bhai J,Billis K,Carvalho-Silva D,Cummins C,Clapham P,Gil L,Giron CG,Gordon L,Hourlier T,Hunt SE,Janacek SH,Juettemann T,Keenan S,Laird MR,Lavidas I,Maurel T,McLaren W,Moore B,Murphy DN,Nag R,Newman V,Nuhn M,Ong CK,Parker A,Patricio M,Riat HS,Sheppard D,Sparrow H,Taylor K,Thormann A,Vullo A,Walts B,Wilder SP,Zadissa A,Kostadima M,Martin FJ,Muffato M,Perry E,Ruffier M,Staines DM,Trevanion SJ,Cunningham F,Yates A,Zerbino DR,Flicek P
Nucleic Acids Res 2016

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TranscriptSNPView: a genome-wide catalog of mouse coding variation.

Cunningham F,Rios D,Griffiths M,Smith J,Ning Z,Cox T,Flicek P,Marin-Garcin P,Herrero J,Rogers J,van der Weyden L,Bradley A,Birney E,Adams DJ
Nat Genet 2006

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Ensembl 2016.

Yates A,Akanni W,Amode MR,Barrell D,Billis K,Carvalho-Silva D,Cummins C,Clapham P,Fitzgerald S,Gil L,Giron CG,Gordon L,Hourlier T,Hunt SE,Janacek SH,Johnson N,Juettemann T,Keenan S,Lavidas I,Martin FJ,Maurel T,McLaren W,Murphy DN,Nag R,Nuhn M,Parker A,Patricio M,Pignatelli M,Rahtz M,Riat HS,Sheppard D,Taylor K,Thormann A,Vullo A,Wilder SP,Zadissa A,Birney E,Harrow J,Muffato M,Perry E,Ruffier M,Spudich G,Trevanion SJ,Cunningham F,Aken BL,Zerbino DR,Flicek P
Nucleic Acids Res 2015

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Genome-wide nucleotide-level mammalian ancestor reconstruction.

Paten B,Herrero J,Fitzgerald S,Beal K,Flicek P,Holmes I,Birney E
Genome Res 2008

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The ensembl regulatory build.

Zerbino DR,Wilder SP,Johnson N,Juettemann T,Flicek PR
Genome Biol 2015

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eHive: an artificial intelligence workflow system for genomic analysis.

Severin J,Beal K,Vilella AJ,Fitzgerald S,Schuster M,Gordon L,Ureta-Vidal A,Flicek P,Herrero J
BMC Bioinformatics 2010

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A database and API for variation, dense genotyping and resequencing data.

Rios D,McLaren WM,Chen Y,Birney E,Stabenau A,Flicek P,Cunningham F
BMC Bioinformatics 2010

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Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.

McLaren W,Pritchard B,Rios D,Chen Y,Flicek P,Cunningham F
Bioinformatics 2010

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Ensembl regulation resources.

Zerbino DR,Johnson N,Juetteman T,Sheppard D,Wilder SP,Lavidas I,Nuhn M,Perry E,Raffaillac-Desfosses Q,Sobral D,Keefe D,Graf S,Ahmed I,Kinsella R,Pritchard B,Brent S,Amode R,Parker A,Trevanion S,Birney E,Dunham I,Flicek P
Database (Oxford) 2016

View Paper (PubMed) View Publication

The ensembl regulatory build.

Zerbino DR,Wilder SP,Johnson N,Juettemann T,Flicek PR
Genome Biol 2015

View Paper (PubMed) View Publication

Ensembl 2009.

Hubbard TJ,Aken BL,Ayling S,Ballester B,Beal K,Bragin E,Brent S,Chen Y,Clapham P,Clarke L,Coates G,Fairley S,Fitzgerald S,Fernandez-Banet J,Gordon L,Graf S,Haider S,Hammond M,Holland R,Howe K,Jenkinson A,Johnson N,Kahari A,Keefe D,Keenan S,Kinsella R,Kokocinski F,Kulesha E,Lawson D,Longden I,Megy K,Meidl P,Overduin B,Parker A,Pritchard B,Rios D,Schuster M,Slater G,Smedley D,Spooner W,Spudich G,Trevanion S,Vilella A,Vogel J,White S,Wilder S,Zadissa A,Birney E,Cunningham F,Curwen V,Durbin R,Fernandez-Suarez XM,Herrero J,Kasprzyk A,Proctor G,Smith J,Searle S,Flicek P
Nucleic Acids Res 2008

View Paper (PubMed) View Publication

Touring Ensembl: a practical guide to genome browsing.

Spudich GM,Fernandez-Suarez XM
BMC Genomics 2010

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Genome browsing with Ensembl: a practical overview.

Spudich G,Fernandez-Suarez XM,Birney E
Brief Funct Genomic Proteomic 2007

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Ensembl 2008.

Flicek P,Aken BL,Beal K,Ballester B,Caccamo M,Chen Y,Clarke L,Coates G,Cunningham F,Cutts T,Down T,Dyer SC,Eyre T,Fitzgerald S,Fernandez-Banet J,Graf S,Haider S,Hammond M,Holland R,Howe KL,Howe K,Johnson N,Jenkinson A,Kahari A,Keefe D,Kokocinski F,Kulesha E,Lawson D,Longden I,Megy K,Meidl P,Overduin B,Parker A,Pritchard B,Prlic A,Rice S,Rios D,Schuster M,Sealy I,Slater G,Smedley D,Spudich G,Trevanion S,Vilella AJ,Vogel J,White S,Wood M,Birney E,Cox T,Curwen V,Durbin R,Fernandez-Suarez XM,Herrero J,Hubbard TJ,Kasprzyk A,Proctor G,Smith J,Ureta-Vidal A,Searle S
Nucleic Acids Res 2007

View Paper (PubMed) View Publication

Ensembl's 10th year.

Flicek P,Aken BL,Ballester B,Beal K,Bragin E,Brent S,Chen Y,Clapham P,Coates G,Fairley S,Fitzgerald S,Fernandez-Banet J,Gordon L,Graf S,Haider S,Hammond M,Howe K,Jenkinson A,Johnson N,Kahari A,Keefe D,Keenan S,Kinsella R,Kokocinski F,Koscielny G,Kulesha E,Lawson D,Longden I,Massingham T,McLaren W,Megy K,Overduin B,Pritchard B,Rios D,Ruffier M,Schuster M,Slater G,Smedley D,Spudich G,Tang YA,Trevanion S,Vilella A,Vogel J,White S,Wilder SP,Zadissa A,Birney E,Cunningham F,Dunham I,Durbin R,Fernandez-Suarez XM,Herrero J,Hubbard TJ,Parker A,Proctor G,Smith J,Searle SM
Nucleic Acids Res 2009

View Paper (PubMed) View Publication

Ensembl 2011.

Flicek P,Amode MR,Barrell D,Beal K,Brent S,Chen Y,Clapham P,Coates G,Fairley S,Fitzgerald S,Gordon L,Hendrix M,Hourlier T,Johnson N,Kahari A,Keefe D,Keenan S,Kinsella R,Kokocinski F,Kulesha E,Larsson P,Longden I,McLaren W,Overduin B,Pritchard B,Riat HS,Rios D,Ritchie GR,Ruffier M,Schuster M,Sobral D,Spudich G,Tang YA,Trevanion S,Vandrovcova J,Vilella AJ,White S,Wilder SP,Zadissa A,Zamora J,Aken BL,Birney E,Cunningham F,Dunham I,Durbin R,Fernandez-Suarez XM,Herrero J,Hubbard TJ,Parker A,Proctor G,Vogel J,Searle SM
Nucleic Acids Res 2010

View Paper (PubMed) View Publication

Ensembl 2012.

Flicek P,Amode MR,Barrell D,Beal K,Brent S,Carvalho-Silva D,Clapham P,Coates G,Fairley S,Fitzgerald S,Gil L,Gordon L,Hendrix M,Hourlier T,Johnson N,Kahari AK,Keefe D,Keenan S,Kinsella R,Komorowska M,Koscielny G,Kulesha E,Larsson P,Longden I,McLaren W,Muffato M,Overduin B,Pignatelli M,Pritchard B,Riat HS,Ritchie GR,Ruffier M,Schuster M,Sobral D,Tang YA,Taylor K,Trevanion S,Vandrovcova J,White S,Wilson M,Wilder SP,Aken BL,Birney E,Cunningham F,Dunham I,Durbin R,Fernandez-Suarez XM,Harrow J,Herrero J,Hubbard TJ,Parker A,Proctor G,Spudich G,Vogel J,Yates A,Zadissa A,Searle SM
Nucleic Acids Res 2011

View Paper (PubMed) View Publication

Ensembl 2013.

Flicek P,Ahmed I,Amode MR,Barrell D,Beal K,Brent S,Carvalho-Silva D,Clapham P,Coates G,Fairley S,Fitzgerald S,Gil L,Garcia-Giron C,Gordon L,Hourlier T,Hunt S,Juettemann T,Kahari AK,Keenan S,Komorowska M,Kulesha E,Longden I,Maurel T,McLaren WM,Muffato M,Nag R,Overduin B,Pignatelli M,Pritchard B,Pritchard E,Riat HS,Ritchie GR,Ruffier M,Schuster M,Sheppard D,Sobral D,Taylor K,Thormann A,Trevanion S,White S,Wilder SP,Aken BL,Birney E,Cunningham F,Dunham I,Harrow J,Herrero J,Hubbard TJ,Johnson N,Kinsella R,Parker A,Spudich G,Yates A,Zadissa A,Searle SM
Nucleic Acids Res 2012

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Ensembl 2002: accommodating comparative genomics.

Clamp M,Andrews D,Barker D,Bevan P,Cameron G,Chen Y,Clark L,Cox T,Cuff J,Curwen V,Down T,Durbin R,Eyras E,Gilbert J,Hammond M,Hubbard T,Kasprzyk A,Keefe D,Lehvaslaiho H,Iyer V,Melsopp C,Mongin E,Pettett R,Potter S,Rust A,Schmidt E,Searle S,Slater G,Smith J,Spooner W,Stabenau A,Stalker J,Stupka E,Ureta-Vidal A,Vastrik I,Birney E
Nucleic Acids Res 2003

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EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.

Vilella AJ,Severin J,Ureta-Vidal A,Heng L,Durbin R,Birney E
Genome Res 2008

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Ensembl variation resources.

Chen Y,Cunningham F,Rios D,McLaren WM,Smith J,Pritchard B,Spudich GM,Brent S,Kulesha E,Marin-Garcia P,Smedley D,Birney E,Flicek P
BMC Genomics 2010

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Ensembl 2002: accommodating comparative genomics.

Clamp M,Andrews D,Barker D,Bevan P,Cameron G,Chen Y,Clark L,Cox T,Cuff J,Curwen V,Down T,Durbin R,Eyras E,Gilbert J,Hammond M,Hubbard T,Kasprzyk A,Keefe D,Lehvaslaiho H,Iyer V,Melsopp C,Mongin E,Pettett R,Potter S,Rust A,Schmidt E,Searle S,Slater G,Smith J,Spooner W,Stabenau A,Stalker J,Stupka E,Ureta-Vidal A,Vastrik I,Birney E
Nucleic Acids Res 2003

View Paper (PubMed)

The Ensembl analysis pipeline.

Potter SC,Clarke L,Curwen V,Keenan S,Mongin E,Searle SM,Stabenau A,Storey R,Clamp M
Genome Res 2004

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The Ensembl automatic gene annotation system.

Curwen V,Eyras E,Andrews TD,Clarke L,Mongin E,Searle SM,Clamp M
Genome Res 2004

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