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

被引：892

作者：

Vilella, Albert J. ^{[1
]}

Severin, Jessica ^{[1
]}

Ureta-Vidal, Abel ^{[1
]}

Heng, Li ^{[2
]}

Durbin, Richard ^{[2
]}

Birney, Ewan ^{[1
]}

机构：

[1] EMBL EBI, Cambridge CB10 1SD, England

[2] Wellcome Trust Sanger Inst, Cambridge CB10 1HH, England

来源：

GENOME RESEARCH | 2009年 / 19卷 / 02期

基金：

英国惠康基金;

关键词：

MAXIMUM-LIKELIHOOD; GENOME SEQUENCE; DATABASE; EVOLUTION; INSIGHTS; ALGORITHM; ORTHOLOGS; FAMILIES; PARALOGS;

D O I：

10.1101/gr.073585.107

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We have developed a comprehensive gene orientated phylogenetic resource, EnsemblCompara GeneTrees, based on a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. We developed two novel non-sequence-based metrics of gene tree correctness and benchmarked a number of tree methods. The TreeBeST method from TreeFam shows the best performance in our hands. We also compared this phylogenetic approach to clustering approaches for ortholog prediction, showing a large increase in coverage using the phylogenetic approach. All data are made available in a number of formats and will be kept up to date with the Ensembl project.

引用

页码：327 / 335

页数：9

共 27 条

[1] The genome sequence of Drosophila melanogaster [J].

Adams, MD ;

Celniker, SE ;

Holt, RA ;

Evans, CA ;

Gocayne, JD ;

Amanatides, PG ;

Scherer, SE ;

Li, PW ;

Hoskins, RA ;

Galle, RF ;

George, RA ;

Lewis, SE ;

Richards, S ;

Ashburner, M ;

Henderson, SN ;

Sutton, GG ;

Wortman, JR ;

Yandell, MD ;

Zhang, Q ;

Chen, LX ;

Brandon, RC ;

Rogers, YHC ;

Blazej, RG ;

Champe, M ;

Pfeiffer, BD ;

Wan, KH ;

Doyle, C ;

Baxter, EG ;

Helt, G ;

Nelson, CR ;

Miklos, GLG ;

Abril, JF ;

Agbayani, A ;

An, HJ ;

Andrews-Pfannkoch, C ;

Baldwin, D ;

Ballew, RM ;

Basu, A ;

Baxendale, J ;

Bayraktaroglu, L ;

Beasley, EM ;

Beeson, KY ;

Benos, PV ;

Berman, BP ;

Bhandari, D ;

Bolshakov, S ;

Borkova, D ;

Botchan, MR ;

Bouck, J ;

Brokstein, P .

SCIENCE, 2000, 287 (5461) :2185-2195

[2] The draft genome of Ciona intestinalis:: Insights into chordate and vertebrate origins [J].

Dehal, P ;

Satou, Y ;

Campbell, RK ;

Chapman, J ;

Degnan, B ;

De Tomaso, A ;

Davidson, B ;

Di Gregorio, A ;

Gelpke, M ;

Goodstein, DM ;

Harafuji, N ;

Hastings, KEM ;

Ho, I ;

Hotta, K ;

Huang, W ;

Kawashima, T ;

Lemaire, P ;

Martinez, D ;

Meinertzhagen, IA ;

Necula, S ;

Nonaka, M ;

Putnam, N ;

Rash, S ;

Saiga, H ;

Satake, M ;

Terry, A ;

Yamada, L ;

Wang, HG ;

Awazu, S ;

Azumi, K ;

Boore, J ;

Branno, M ;

Chin-bow, S ;

DeSantis, R ;

Doyle, S ;

Francino, P ;

Keys, DN ;

Haga, S ;

Hayashi, H ;

Hino, K ;

Imai, KS ;

Inaba, K ;

Kano, S ;

Kobayashi, K ;

Kobayashi, M ;

Lee, BI ;

Makabe, KW ;

Manohar, C ;

Matassi, G ;

Medina, M .

SCIENCE, 2002, 298 (5601) :2157-2167

[3] A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database [J].

Dehal, Paramvir S. ;

Boore, Jeffrey L. .

BMC BIOINFORMATICS, 2006, 7 (1)

[4] Tree pattern matching in phylogenetic trees:: automatic search for orthologs or paralogs in homologous gene sequence databases [J].

Dufayard, JF ;

Duret, L ;

Penel, S ;

Gouy, M ;

Rechenmann, F ;

Perrière, G .

BIOINFORMATICS, 2005, 21 (11) :2596-2603

[5] MUSCLE: a multiple sequence alignment method with reduced time and space complexity [J].

Edgar, RC .

BMC BIOINFORMATICS, 2004, 5 (1) :1-19

[6] An efficient algorithm for large-scale detection of protein families [J].

Enright, AJ ;

Van Dongen, S ;

Ouzounis, CA .

NUCLEIC ACIDS RESEARCH, 2002, 30 (07) :1575-1584

[7] MSOAR: A high-throughput ortholog assignment system based on genome rearrangement [J].

Fu, Zheng ;

Chen, Xin ;

Vacic, Vladimir ;

Nan, Peng ;

Zhong, Yang ;

Jiang, Tao .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2007, 14 (09) :1160-1175

[8] Genome sequence of the Brown Norway rat yields insights into mammalian evolution [J].

Gibbs, RA ;

Weinstock, GM ;

Metzker, ML ;

Muzny, DM ;

Sodergren, EJ ;

Scherer, S ;

Scott, G ;

Steffen, D ;

Worley, KC ;

Burch, PE ;

Okwuonu, G ;

Hines, S ;

Lewis, L ;

DeRamo, C ;

Delgado, O ;

Dugan-Rocha, S ;

Miner, G ;

Morgan, M ;

Hawes, A ;

Gill, R ;

Holt, RA ;

Adams, MD ;

Amanatides, PG ;

Baden-Tillson, H ;

Barnstead, M ;

Chin, S ;

Evans, CA ;

Ferriera, S ;

Fosler, C ;

Glodek, A ;

Gu, ZP ;

Jennings, D ;

Kraft, CL ;

Nguyen, T ;

Pfannkoch, CM ;

Sitter, C ;

Sutton, GG ;

Venter, JC ;

Woodage, T ;

Smith, D ;

Lee, HM ;

Gustafson, E ;

Cahill, P ;

Kana, A ;

Doucette-Stamm, L ;

Weinstock, K ;

Fechtel, K ;

Weiss, RB ;

Dunn, DM ;

Green, ED .

NATURE, 2004, 428 (6982) :493-521

[9] Evolutionary and biomedical insights from the rhesus macaque genome [J].

Gibbs, Richard A. ;

Rogers, Jeffrey ;

Katze, Michael G. ;

Bumgarner, Roger ;

Weinstock, George M. ;

Mardis, Elaine R. ;

Remington, Karin A. ;

Strausberg, Robert L. ;

Venter, J. Craig ;

Wilson, Richard K. ;

Batzer, Mark A. ;

Bustamante, Carlos D. ;

Eichler, Evan E. ;

Hahn, Matthew W. ;

Hardison, Ross C. ;

Makova, Kateryna D. ;

Miller, Webb ;

Milosavljevic, Aleksandar ;

Palermo, Robert E. ;

Siepel, Adam ;

Sikela, James M. ;

Attaway, Tony ;

Bell, Stephanie ;

Bernard, Kelly E. ;

Buhay, Christian J. ;

Chandrabose, Mimi N. ;

Dao, Marvin ;

Davis, Clay ;

Delehaunty, Kimberly D. ;

Ding, Yan ;

Dinh, Huyen H. ;

Dugan-Rocha, Shannon ;

Fulton, Lucinda A. ;

Gabisi, Ramatu Ayiesha ;

Garner, Toni T. ;

Godfrey, Jennifer ;

Hawes, Alicia C. ;

Hernandez, Judith ;

Hines, Sandra ;

Holder, Michael ;

Hume, Jennifer ;

Jhangiani, Shalini N. ;

Joshi, Vandita ;

Khan, Ziad Mohid ;

Kirkness, Ewen F. ;

Cree, Andrew ;

Fowler, R. Gerald ;

Lee, Sandra ;

Lewis, Lora R. ;

Li, Zhangwan .

SCIENCE, 2007, 316 (5822) :222-234

[10] Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human [J].

Goodstadt, Leo ;

Ponting, Chris P. .

PLOS COMPUTATIONAL BIOLOGY, 2006, 2 (09) :1134-1150

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