OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

被引：123

作者：

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

Train, Clement-Marie ^{[3
]}

Gilbert, Kimberly J. ^{[1
,3
,4
]}

Mediratta, Ishita ^{[3
,5
]}

de Farias, Tarcisio Mendes ^{[1
]}

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

Nevers, Yannis ^{[1
,3
,4
]}

Radoykova, Hale-Seda ^{[6
,7
]}

Rossier, Victor ^{[1
,3
,4
]}

Vesztrocy, Alex Warwick ^{[1
,3
,4
]}

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

Dessimoz, Christophe ^{[1
,3
,4
,6
,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, Dept Computat Biol, CH-1015 Lausanne, Switzerland

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

[5] BITS Pilani, Dept Comp Sci & Informat Syst, KK Birla Goa Campus, Sancoale, Goa, India

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

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

来源：

NUCLEIC ACIDS RESEARCH | 2021年 / 49卷 / D1期

基金：

瑞士国家科学基金会;

关键词：

EVOLUTION; DATABASE;

D O I：

10.1093/nar/gkaa1007

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：

OMA is an established resource to elucidate evolutionary relationships among genes from currently 2326 genomes covering all domains of life. OMA provides pairwise and groupwise orthologs, functional annotations, local and global gene order conservation (synteny) information, among many other functions. This update paper describes the reorganisation of the database into gene-, group- and genome-centric pages. Other new and improved features are detailed, such as reporting of the evolutionarily best conserved isoforms of alternatively spliced genes, the inferred local order of ancestral genes, phylogenetic profiling, better cross-references, fast genome mapping, semantic data sharing via RDF, as well as a special coronavirus OMA with 119 viruses from the Nidovirales order, including SARS-CoV-2, the agent of the COVID-19 pandemic. We conclude with improvements to the documentation of the resource through primers, tutorials and short videos. OMA is accessible at https://omabrowser.org.

引用

页码：D373 / D379

页数：7

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