Altenhoff Adrian M, Škunca Nives, Glover Natasha, Train Clément-Marie, Sueki Anna, Piližota Ivana, Gori Kevin, Tomiczek Bartlomiej, Müller Steven, Redestig Henning, Gonnet Gaston H, Dessimoz Christophe
University College London, Gower Street, London WC1E 6BT, UK Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland.
University College London, Gower Street, London WC1E 6BT, UK Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France Bayer CropScience NV, Technologiepark 38, 9052 Gent, Belgium.
Nucleic Acids Res. 2015 Jan;43(Database issue):D240-9. doi: 10.1093/nar/gku1158. Epub 2014 Nov 15.
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.
直系同源矩阵（OMA）项目是一种方法及相关数据库，用于推断目前1706个完整蛋白质组之间的进化关系（即所有基因组中每个蛋白质编码基因对应的蛋白质序列）。在这篇更新文章中，我们介绍了OMA的六项主要新进展：（i）一个新的网络界面；（ii）作为OMA流程一部分的基因本体功能预测；（iii）对植物基因组，特别是小麦基因组中的同源基因有更好的支持；（iv）一个新的共线性查看器，可提供直系同源基因的基因组背景；（v）可下载OrthXML格式的静态计算分层直系同源组子集；（vi）能够导出全对全计算的部分内容，并将其与自定义数据相结合，用于“客户端”直系同源预测。可通过OMA浏览器以及位于http://omabrowser.org的各种编程接口访问OMA。
