The Ensembl gene annotation system

被引：524

作者：

Aken, Bronwen L. ^{[1
,2
]}

Ayling, Sarah ^{[2
,3
]}

Barrell, Daniel ^{[1
,2
,4
]}

Clarke, Laura ^{[2
,5
]}

Curwen, Valery ^{[2
]}

Fairley, Susan ^{[2
,5
]}

Banet, Julio Fernandez ^{[2
,6
]}

Billis, Konstantinos ^{[1
,2
]}

Giron, Carlos Garcia ^{[1
,2
]}

Hourlier, Thibaut ^{[1
,2
]}

Howe, Kevin ^{[2
,5
]}

Kahari, Andreas ^{[2
,7
]}

Kokocinski, Felix ^{[2
]}

Martin, Fergal J. ^{[1
,2
]}

Murphy, Daniel N. ^{[1
,2
]}

Nag, Rishi ^{[1
,2
]}

Ruffier, Magali ^{[2
,5
]}

Schuster, Michael ^{[1
,8
]}

Tang, Y. Amy ^{[2
,5
]}

Vogel, Jan-Hinnerk ^{[2
,9
]}

White, Simon ^{[2
,10
]}

Zadissa, Amonida ^{[2
,5
]}

Flicek, Paul ^{[1
,2
]}

Searle, Stephen M. J. ^{[2
]}

机构：

[1] European Bioinformat Inst Wellcome Genome Campus, European Mol Biol Lab, Cambridge CB10 1SD, England

[2] Wellcome Trust Sanger Inst Wellcome Genome Campus, Cambridge CB10 1SA, England

[3] Genome Anal Ctr, Norwich Res Pk, Norwich NR4 7UH, Norfolk, England

[4] Eagle Genom Ltd, Babraham Res Campus, Cambridge CB22 3AT, England

[5] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England

[6] Pfizer Inc, 10646 Sci Ctr Dr, San Diego, CA 92121 USA

[7] Uppsala Univ, Inst Cell Molekylarbiol, Husargatan 3, S-75237 Uppsala, Sweden

[8] Austrian Acad Sci, CeMM Res Ctr Mol Med, A-1090 Vienna, Austria

[9] Genentech Inc, 1 DNAWay, San Francisco, CA 94080 USA

[10] Baylor Coll Med, Human Genome Sequencing Ctr, Houston, TX 77030 USA

来源：

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | 2016年

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

GENOME PROVIDES INSIGHTS; SEQUENCE; REVEALS; EVOLUTION; ALIGNMENT; DATABASE; ZEBRAFISH; IDENTIFICATION; COMPLEXITY; GENERATION;

D O I：

10.1093/database/baw093

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.

引用

页数：19

共 106 条

[1] The genome of the green anole lizard and a comparative analysis with birds and mammals
Alfoeldi, Jessica
Di Palma, Federica
Grabherr, Manfred
Williams, Christina
Kong, Lesheng
Mauceli, Evan
Russell, Pamela
Lowe, Craig B.
Glor, Richard E.
Jaffe, Jacob D.
Ray, David A.
Boissinot, Stephane
Shedlock, Andrew M.
Botka, Christopher
Castoe, Todd A.
Colbourne, John K.
Fujita, Matthew K.
Moreno, Ricardo Godinez
ten Hallers, Boudewijn F.
Haussler, David
Heger, Andreas
Heiman, David
Janes, Daniel E.
Johnson, Jeremy
de Jong, Pieter J.
Koriabine, Maxim Y.
Lara, Marcia
Novick, Peter A.
Organ, Chris L.
Peach, Sally E.
Poe, Steven
Pollock, David D.
de Queiroz, Kevin
Sanger, Thomas
Searle, Steve
Smith, Jeremy D.
Smith, Zachary
Swofford, Ross
Turner-Maier, Jason
Wade, Juli
Young, Sarah
Zadissa, Amonida
Edwards, Scott V.
Glenn, Travis C.
Schneider, Christopher J.
Losos, Jonathan B.
Lander, Eric S.
Breen, Matthew
Ponting, Chris P.
Lindblad-Toh, Kerstin
[J]. NATURE, 2011, 477 (7366) : 587 - 591
[2] BASIC LOCAL ALIGNMENT SEARCH TOOL
ALTSCHUL, SF
GISH, W
MILLER, W
MYERS, EW
LIPMAN, DJ
[J]. JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) : 403 - 410
[3] OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders
Amberger, Joanna S.
Bocchini, Carol A.
Schiettecatte, Francois
Scott, Alan F.
Hamosh, Ada
[J]. NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) : D789 - D798
[4] The African coelacanth genome provides insights into tetrapod evolution
Amemiya, Chris T.
Alfoeldi, Jessica
Lee, Alison P.
Fan, Shaohua
Philippe, Herve
MacCallum, Iain
Braasch, Ingo
Manousaki, Tereza
Schneider, Igor
Rohner, Nicolas
Organ, Chris
Chalopin, Domitille
Smith, Jeramiah J.
Robinson, Mark
Dorrington, Rosemary A.
Gerdol, Marco
Aken, Bronwen
Biscotti, Maria Assunta
Barucca, Marco
Baurain, Denis
Berlin, Aaron M.
Blatch, Gregory L.
Buonocore, Francesco
Burmester, Thorsten
Campbell, Michael S.
Canapa, Adriana
Cannon, John P.
Christoffels, Alan
De Moro, Gianluca
Edkins, Adrienne L.
Fan, Lin
Fausto, Anna Maria
Feiner, Nathalie
Forconi, Mariko
Gamieldien, Junaid
Gnerre, Sante
Gnirke, Andreas
Goldstone, Jared V.
Haerty, Wilfried
Hahn, Mark E.
Hesse, Uljana
Hoffmann, Steve
Johnson, Jeremy
Karchner, Sibel I.
Kuraku, Shigehiro
Lara, Marcia
Levin, Joshua Z.
Litman, Gary W.
Mauceli, Evan
Miyake, Tsutomu
[J]. NATURE, 2013, 496 (7445) : 311 - 316
[5] [Anonymous], GENOME BIOL S1
[6] [Anonymous], BIOASSAYS
[7] Activities at the Universal Protein Resource (UniProt)
Apweiler, Rolf
Bateman, Alex
Martin, Maria Jesus
O'Donovan, Claire
Magrane, Michele
Alam-Faruque, Yasmin
Alpi, Emanuele
Antunes, Ricardo
Arganiska, Joanna
Casanova, Elisabet Barrera
Bely, Benoit
Bingley, Mark
Bonilla, Carlos
Britto, Ramona
Bursteinas, Borisas
Chan, Wei Mun
Chavali, Gayatri
Cibrian-Uhalte, Elena
Da Silva, Alan
De Giorgi, Maurizio
Dogan, Tunca
Fazzini, Francesco
Gane, Paul
Castro, Leyla Garcia
Garmiri, Penelope
Hatton-Ellis, Emma
Hieta, Reija
Huntley, Rachael
Legge, Duncan
Liu, Wudong
Luo, Jie
MacDougall, Alistair
Mutowo, Prudence
Nightingale, Andrew
Orchard, Sandra
Pichler, Klemens
Poggioli, Diego
Pundir, Sangya
Pureza, Luis
Qi, Guoying
Rosanoff, Steven
Saidi, Rabie
Sawford, Tony
Shypitsyna, Aleksandra
Turner, Edward
Volynkin, Vladimir
Wardell, Tony
Watkins, Xavier
Zellner, Hermann
Corbett, Matt
[J]. NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) : D191 - D198
[8] Melanocortin 4 receptor mutations contribute to the adaptation of cavefish to nutrient-poor conditions
Aspiras, Ariel C.
Rohner, Nicolas
Martineau, Brian
Borowsky, Richard L.
Tabin, Clifford J.
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (31) : 9668 - 9673
[9] The PRINTS database: a fine-grained protein sequence annotation and analysis resource-its status in 2012
Attwood, Teresa K.
Coletta, Alain
Muirhead, Gareth
Pavlopoulou, Athanasia
Philippou, Peter B.
Popov, Ivan
Roma-Mateo, Carlos
Theodosiou, Athina
Mitchell, Alex L.
[J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2012,
[10] GenBank
Benson, Dennis A.
Clark, Karen
Karsch-Mizrachi, Ilene
Lipman, David J.
Ostell, James
Sayers, Eric W.
[J]. NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) : D32 - D37

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