OrthoDB: the hierarchical catalog of eukaryotic orthologs

被引：80

作者：

Kriventseva, Evgenia V. ^{[3
]}

Rahman, Nazim ^{[1
]}

Espinosa, Octavio ^{[1
]}

Zdobnov, Evgeny M. ^{[1
,2
,4
]}

机构：

[1] Univ Geneva, Sch Med, Dept Genet Med & Dev, CH-1211 Geneva, Switzerland

[2] Univ Geneva, Sch Med, Swiss Inst Bioinformat, CH-1211 Geneva, Switzerland

[3] Univ Geneva, Dept Struct Biol & Bioinformat, CH-1211 Geneva, Switzerland

[4] Imperial Coll London, London SW7 24Z, England

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

关键词：

D O I：

10.1093/nar/gkm845

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：

The concept of orthology is widely used to relate genes across different species using comparative genomics, and it provides the basis for inferring gene function. Here we present the web accessible OrthoDB database that catalogs groups of orthologous genes in a hierarchical manner, at each radiation of the species phylogeny, from more general groups to more fine-grained delineations between closely related species. We used a COG-like and Inparanoid-like ortholog delineation procedure on the basis of all-against-all Smith-Waterman sequence comparisons to analyze 58 eukaryotic genomes, focusing on vertebrates, insects and fungi to facilitate further comparative studies. The database is freely available at http://cegg.unige.ch/orthodb.

引用

页码：D271 / D275

页数：5

共 29 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] 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

[3] Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis [J].

Castresana, J .

MOLECULAR BIOLOGY AND EVOLUTION, 2000, 17 (04) :540-552

[4] Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes [J].

Chen, Feng ;

Mackey, Aaron J. ;

Vermunt, Jeroen K. ;

Roos, David S. .

PLOS ONE, 2007, 2 (04)

[5] OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups [J].

Chen, Feng ;

Mackey, Aaron J. ;

Stoeckert, Christian J., Jr. ;

Roos, David S. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D363-D368

[6]

DAYHOFF MO, 1976, FED PROC, V35, P2132

[7] HOVERGEN - A DATABASE OF HOMOLOGOUS VERTEBRATE GENES [J].

DURET, L ;

MOUCHIROUD, D ;

GOUY, M .

NUCLEIC ACIDS RESEARCH, 1994, 22 (12) :2360-2365

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

Edgar, RC .

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

[9] DISTINGUISHING HOMOLOGOUS FROM ANALOGOUS PROTEINS [J].

FITCH, WM .

SYSTEMATIC ZOOLOGY, 1970, 19 (02) :99-&

[10] PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference [J].

Guindon, S ;

Lethiec, F ;

Duroux, P ;

Gascuel, O .

NUCLEIC ACIDS RESEARCH, 2005, 33 :W557-W559

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