TreeFam:: a curated database of phylogenetic trees of animal gene families

被引：393

作者：

Li, Heng

Coghlan, Avril

Ruan, Jue

Coin, Lachlan James

Heriche, Jean-Karim

Osmotherly, Lara

Li, Ruiqiang

Liu, Tao

Zhang, Zhang

Bolund, Lars

Wong, Gane Ka-Shu

Zheng, Weimou

Dehal, Paramvir

Wang, Jun

Durbin, Richard

机构：

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

[2] Chinese Acad Sci, Beijing Inst Gen, Beijing Gen Inst, Beijing 101300, Peoples R China

[3] Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China

[4] Univ Aarhus, Inst Human Genet, DK-8000 Aarhus C, Denmark

[5] Univ So Denmark, Dept Biochem & Mol Biol, DK-5230 Odense M, Denmark

[6] Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China

[7] Univ Washington, Dept Med, Genome Ctr, Seattle, WA 98195 USA

[8] Joint Genome Inst, Evolutionary Gen Dept, Dept Energy, Walnut Creek, CA USA

[9] Lawrence Berkeley Lab, Walnut Creek, CA USA

来源：

NUCLEIC ACIDS RESEARCH | 2006年 / 34卷

关键词：

D O I：

10.1093/nar/gkj118

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：

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families 25 and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; similar to 40 - 85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at http://www.treefam.org and http://treefam.genomics.org.cn.

引用

页码：D572 / D580

页数：9

共 46 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] Bayesian gene/species tree reconciliation and orthology analysis using MCMC [J].

Arvestad, Lars ;

Berglund, Ann-Charlotte ;

Lagergren, Jens ;

Sennblad, Bengt .

BIOINFORMATICS, 2003, 19 :i7-i15

[3] The universal protein resource (UniProt) [J].

Bairoch, Amos ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Puy, Ghislaine Argoud ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

deCastro, Edouard ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

Dobrokhotov, Pavel ;

Dornevil, Dolnide ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Feuermann, Marc ;

Gehant, Sebastian ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

Ioannidis, Vassilios ;

Ivanyi, Ivan ;

James, Janet ;

Jain, Eric ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra ;

Lara, Vicente ;

Lemercier, Philippe ;

Le Saux, Virginie .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D193-D197

[4] Fungal BLAST and Model Organism BLASTP Best Hits:: new comparison resources at the Saccharomyces Genome Database (SGD) [J].

Balakrishnan, R ;

Christie, KR ;

Costanzo, MC ;

Dolinski, K ;

Dwight, SS ;

Engel, SR ;

Fisk, DG ;

Hirschman, JE ;

Hong, EL ;

Nash, R ;

Oughtred, R ;

Skrzypek, M ;

Theesfeld, CL ;

Binkley, G ;

Dong, Q ;

Lane, C ;

Sethuraman, A ;

Weng, S ;

Botstein, D ;

Cherry, JM .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D374-D377

[5]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkr1065, 10.1093/nar/gkh121]

[6] Genomes OnLine Database (GOLD): a monitor of genome projects world-wide [J].

Bernal, A ;

Ear, U ;

Kyrpides, N .

NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :126-127

[7] Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees [J].

Chen, FC ;

Li, WH .

AMERICAN JOURNAL OF HUMAN GENETICS, 2001, 68 (02) :444-456

[8] Pseudo-likelhood ratio tests for semiparametric multivariate copula model selection [J].

Chen, XH ;

Fan, YQ .

CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE, 2005, 33 (03) :389-414

[9] The Jalview Java']Java alignment editor [J].

Clamp, M ;

Cuff, J ;

Searle, SM ;

Barton, GJ .

BIOINFORMATICS, 2004, 20 (03) :426-427

[10] Two rounds of whole genome duplication in the ancestral vertebrate [J].

Dehal, P ;

Boore, JL .

PLOS BIOLOGY, 2005, 3 (10) :1700-1708

← 1 2 3 4 5 →