Tegenfeldt Fredrik, Kuznetsov Dmitry, Manni Mosè, Berkeley Matthew, Zdobnov Evgeny M, Kriventseva Evgenia V
Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.
Nucleic Acids Res. 2025 Jan 6;53(D1):D516-D522. doi: 10.1093/nar/gkae987.
OrthoDB (https://www.orthodb.org) offers evolutionary and functional annotations of orthologous genes in the widest sampling of eukaryotes, prokaryotes, and viruses, extending experimental gene function knowledge to newly sequenced genomes. We collect gene annotations, delineate hierarchical gene orthology and annotate the orthologous groups (OGs) with functional and evolutionary traits. OrthoDB is the leading resource for species diversity, striving to sample the most diverse and well-researched organisms with the highest quality genomic data. This update expands to include 5827 eukaryotic genomes. We have also added coding DNA sequences (CDSs) and gene loci coordinates. OrthoDB can be browsed, downloaded, or accessed using REST API, SPARQL/RDF and now also via API packages for Python and R Bioconductor. OrthoLoger (https://orthologer.ezlab.org), the tool used for inferring orthologs in OrthoDB, is now available as a Conda package and through BioContainers. ODB-mapper, a component of OrthoLoger, streamlines annotation of genes from newly sequenced genomes with OrthoDB evolutionary and functional descriptors. The benchmarking sets of universal single-copy orthologs (BUSCO), derived from OrthoDB, had correspondingly a major update. The BUSCO tool (https://busco.ezlab.org) has become a standard in genomics, uniquely capable of assessing both eukaryotic and prokaryotic species. It is applicable to gene sets, transcriptomes, genome assemblies and metagenomic bins.
OrthoDB（https://www.orthodb.org）提供了真核生物、原核生物和病毒最广泛样本中直系同源基因的进化和功能注释，将实验性基因功能知识扩展到新测序的基因组。我们收集基因注释，划定基因直系同源关系的层次结构，并用功能和进化特征注释直系同源组（OGs）。OrthoDB是物种多样性的主要资源，致力于用最高质量的基因组数据对最多样化且研究充分的生物体进行采样。此次更新扩展到包括5827个真核生物基因组。我们还添加了编码DNA序列（CDS）和基因座坐标。可以通过REST API、SPARQL/RDF浏览、下载或访问OrthoDB，现在还可以通过用于Python和R Bioconductor的API包进行访问。OrthoLoger（https://orthologer.ezlab.org）是用于在OrthoDB中推断直系同源基因的工具，现在可以作为Conda包并通过BioContainers获取。ODB-mapper是OrthoLoger的一个组件，它利用OrthoDB的进化和功能描述符简化了对新测序基因组中基因的注释。源自OrthoDB的通用单拷贝直系同源基因（BUSCO）基准集也相应地进行了重大更新。BUSCO工具（https://busco.ezlab.org）已成为基因组学的标准，能够独特地评估真核生物和原核生物物种。它适用于基因集、转录组、基因组组装和宏基因组 bins。
