The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

被引：147

作者：

Altenhoff, Adrian M. ^{[1
,2
,3
]}

Skunca, Nives ^{[1
,2
,3
]}

Glover, Natasha ^{[1
,4
,5
]}

Train, Clement-Marie ^{[3
]}

Sueki, Anna ^{[1
]}

Pilizota, Ivana ^{[1
]}

Gori, Kevin ^{[6
]}

Tomiczek, Bartlomiej ^{[1
]}

Mueller, Steven ^{[1
]}

Redestig, Henning ^{[5
]}

Gonnet, Gaston H. ^{[2
,3
]}

Dessimoz, Christophe ^{[1
,6
]}

机构：

[1] UCL, London WC1E 6BT, England

[2] Swiss Inst Bioinformat, CH-8092 Zurich, Switzerland

[3] Swiss Fed Inst Technol, CH-8092 Zurich, Switzerland

[4] INRA, Genet Divers & Ecophysiol Cereals UMR1095, F-63039 Clermont Ferrand, France

[5] Bayer CropSci NV, B-9052 Ghent, Belgium

[6] European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England

来源：

NUCLEIC ACIDS RESEARCH | 2015年 / 43卷 / D1期

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：

COMPARATIVE GENOMICS; GENE; EVOLUTION; DIVERSITY; PROTEINS; SEQUENCE; ENSEMBL; CONTEXT; FAMILY; PLAZA;

D O I：

10.1093/nar/gku1158

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 Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes). In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction. OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org.

引用

页码：D240 / D249

页数：10

共 49 条

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