The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces

被引：155

作者：

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

Glover, Natasha M. ^{[1
,3
,4
]}

Train, Clement-Marie ^{[1
,3
,4
]}

Kaleb, Klara ^{[5
]}

Vesztrocy, Alex Warwick ^{[1
,5
]}

Dylus, David ^{[1
,3
,4
]}

de Farias, Tarcisio M. ^{[1
,3
,4
]}

Zile, Karina ^{[1
,5
]}

Stevenson, Charles ^{[5
]}

Long, Jiao ^{[6
]}

Redestig, Henning ^{[6
]}

Gonnet, Gaston H. ^{[1
,2
]}

Dessimoz, Christophe ^{[1
,3
,4
,5
,7
]}

机构：

[1] SIB Swiss Inst Bioinformat, CH-1015 Lausanne, Switzerland

[2] Swiss Fed Inst Technol, Comp Sci, Univ Str 6, CH-8092 Zurich, Switzerland

[3] Univ Lausanne, Ctr Integrat Genom, CH-1015 Lausanne, Switzerland

[4] Univ Lausanne, Dept Computat Biol, CH-1015 Lausanne, Switzerland

[5] UCL, Dept Genet Evolut & Environm, Gower St, London WC1E 6BT, England

[6] Bayer Crop Sci NV, Technol Pk 38, B-9052 Ghent, Belgium

[7] UCL, Dept Comp Sci, Gower St, London WC1E 6BT, England

来源：

NUCLEIC ACIDS RESEARCH | 2018年 / 46卷 / D1期

基金：

英国生物技术与生命科学研究理事会;

关键词：

FUNCTIONAL ANNOTATIONS; PHYLOGENETIC TREES; SEQUENCE; FRAMEWORK; UPDATE;

D O I：

10.1093/nar/gkx1019

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) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new features in the OMA web browser. Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources. OMA can be freely accessed at https://omabrowser.org.

引用

页码：D477 / D485

页数：9

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