SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland.
Nucleic Acids Res. 2024 Jan 5;52(D1):D513-D521. doi: 10.1093/nar/gkad1020.
In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particularly an expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pages and an Ancestral Gene Order viewer, allowing users to explore the evolutionary history and gene content of ancestral genomes. We also introduce a revamped Local Synteny Viewer to compare genomic neighborhoods across both extant and ancestral genomes. Hierarchical Orthologous Groups (HOGs) are now annotated with Gene Ontology annotations, and users can easily perform extant or ancestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem, including OMAmer for proteome mapping, OMArk for proteome quality assessment, OMAMO for model organism selection and Read2Tree for phylogenetic species tree construction from reads. These new features provide exciting opportunities for orthology analysis and comparative genomics. OMA is accessible at https://omabrowser.org.
在这篇更新论文中，我们介绍了 OMA 浏览器知识库的最新进展，旨在提供高质量的同源推断，并促进基因家族、基因组及其进化的研究。首先，我们讨论了数据库中新增的物种，特别是对原核生物物种的更全面表示。OMA 浏览器现在提供了祖先基因组页面和祖先基因排序查看器，使用户能够探索祖先基因组的进化历史和基因内容。我们还引入了经过改进的局部同线性查看器，以比较现存和祖先基因组的基因组邻域。层次同源群（HOGs）现在都有基因本体论注释，用户可以轻松地进行现存或祖先的 GO 富集分析。最后，我们总结了 OMA 生态系统中的新工具，包括用于蛋白质组映射的 OMAmer、用于蛋白质组质量评估的 OMArk、用于模式生物选择的 OMAMO 以及用于从读取数据构建系统发育种系发生树的 Read2Tree。这些新功能为同源分析和比较基因组学提供了令人兴奋的机会。OMA 可在 https://omabrowser.org 上访问。
Zotero 插件
