The Ensembl gene annotation system

被引：523

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

[21] Facing growth in the European Nucleotide Archive
Cochrane, Guy
Alako, Blaise
Amid, Clara
Bower, Lawrence
Cerdeno-Tarraga, Ana
Cleland, Iain
Gibson, Richard
Goodgame, Neil
Jang, Mikyung
Kay, Simon
Leinonen, Rasko
Lin, Xiu
Lopez, Rodrigo
McWilliam, Hamish
Oisel, Arnaud
Pakseresht, Nima
Pallreddy, Swapna
Park, Youngmi
Plaister, Sheila
Radhakrishnan, Rajesh
Riviere, Stephane
Rossello, Marc
Senf, Alexander
Silvester, Nicole
Smirnov, Dmitriy
ten Hoopen, Petra
Toribio, Ana
Vaughan, Daniel
Zalunin, Vadim
[J]. NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) : D30 - D35
[22] Incorporating RNA-seq data into the zebrafish Ensembl genebuild
Collins, John E.
White, Simon
Searle, Stephen M. J.
Stemple, Derek L.
[J]. GENOME RESEARCH, 2012, 22 (10) : 2067 - 2078
[23] The Ensembl automatic gene annotation system
Curwen, V
Eyras, E
Andrews, TD
Clarke, L
Mongin, E
Searle, SMJ
Clamp, M
[J]. GENOME RESEARCH, 2004, 14 (05) : 942 - 950
[24] Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
Dalloul, Rami A.
Long, Julie A.
Zimin, Aleksey V.
Aslam, Luqman
Beal, Kathryn
Blomberg, Le Ann
Bouffard, Pascal
Burt, David W.
Crasta, Oswald
Crooijmans, Richard P. M. A.
Cooper, Kristal
Coulombe, Roger A.
De, Supriyo
Delany, Mary E.
Dodgson, Jerry B.
Dong, Jennifer J.
Evans, Clive
Frederickson, Karin M.
Flicek, Paul
Florea, Liliana
Folkerts, Otto
Groenen, Martien A. M.
Harkins, Tim T.
Herrero, Javier
Hoffmann, Steve
Megens, Hendrik-Jan
Jiang, Andrew
de Jong, Pieter
Kaiser, Pete
Kim, Heebal
Kim, Kyu-Won
Kim, Sungwon
Langenberger, David
Lee, Mi-Kyung
Lee, Taeheon
Mane, Shrinivasrao
Marcais, Guillaume
Marz, Manja
McElroy, Audrey P.
Modise, Thero
Nefedov, Mikhail
Notredame, Cedric
Paton, Ian R.
Payne, William S.
Pertea, Geo
Prickett, Dennis
Puiu, Daniela
Qioa, Dan
Raineri, Emanuele
Ruffier, Magali
[J]. PLOS BIOLOGY, 2010, 8 (09)
[25] Computational identification of promoters and first exons in the human genome
Davuluri, RV
Grosse, I
Zhang, MQ
[J]. NATURE GENETICS, 2001, 29 (04) : 412 - 417
[26] DENMAN RB, 1993, BIOTECHNIQUES, V15, P1090
[27] Computational detection and location of transcription start sites in mammalian genomic DNA
Down, TA
Hubbard, TJP
[J]. GENOME RESEARCH, 2002, 12 (03) : 458 - 461
[28] A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
Eddy, SR
[J]. BMC BIOINFORMATICS, 2002, 3 (1)
[29] The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution
Elsik, Christine G.
Tellam, Ross L.
Worley, Kim C.
Gibbs, Richard A.
Abatepaulo, Antonio R. R.
Abbey, Colette A.
Adelson, David L.
Aerts, Jan
Ahola, Virpi
Alexander, Lee
Alioto, Tyler
Almeida, Iassudara G.
Amadio, Ariel F.
Anatriello, Elen
Antonarakis, Stylianos E.
Anzola, Juan M.
Astashyn, Alex
Bahadue, Suria M.
Baldwin, Cynthia L.
Barris, Wes
Baxter, Rebecca
Bell, Stephanie Nicole
Bennett, Anna K.
Bennett, Gary L.
Biase, Fernando H.
Boldt, Clayton R.
Bradley, Daniel G.
Brinkman, Fiona S. L.
Brinkmeyer-Langford, Candice L.
Brown, Wendy C.
Brownstein, Michael J.
Buhay, Christian
Caetano, Alexandre R.
Camara, Francisco
Carroll, Jeffrey A.
Carvalho, Wanessa A.
Casey, Theresa
Cervelatti, Elaine P.
Chack, Joseph
Chacko, Elsa
Chandrabose, Mimi M.
Chapin, Jennifer E.
Chapple, Charles E.
Chen, Hsiu-Chuan
Chen, Lin
Cheng, Ye
Cheng, Ze
Childers, Christopher P.
Chitko-McKown, Carol G.
Chiu, Readman
[J]. SCIENCE, 2009, 324 (5926) : 522 - 528
[30] Pfam: the protein families database
Finn, Robert D.
Bateman, Alex
Clements, Jody
Coggill, Penelope
Eberhardt, Ruth Y.
Eddy, Sean R.
Heger, Andreas
Hetherington, Kirstie
Holm, Liisa
Mistry, Jaina
Sonnhammer, Erik L. L.
Tate, John
Punta, Marco
[J]. NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) : D222 - D230

← 1 2 3 4 5 6 7 8 9 10 →