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.

中文翻译：

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OrthoDB 和 BUSCO 更新：具有更广泛基因组采样的直系同源物注释


OrthoDB （https://www.orthodb.org） 在最广泛的真核生物、原核生物和病毒样本中提供直系同源基因的进化和功能注释，将实验基因功能知识扩展到新测序的基因组。我们收集基因注释，描绘分层基因正交，并用功能和进化特征注释直系同源组 （OG）。OrthoDB 是物种多样性的领先资源，致力于以最高质量的基因组数据对最多样化和研究最充分的生物体进行采样。此更新扩展为包括 5827 个真核基因组。我们还添加了编码 DNA 序列 （CDS） 和基因位点坐标。可以使用 REST API、SPARQL/RDF 浏览、下载或访问 OrthoDB，现在还可以通过 Python 和 R Bioconductor 的 API 包进行浏览、下载或访问。OrthoLoger （https://orthologer.ezlab.org） 是用于在 OrthoDB 中推断直系同源物的工具，现在以 Conda 包的形式提供，也可以通过 BioContainers 获得。ODB-mapper 是 OrthoLoger 的一个组件，它使用 OrthoDB 进化和功能描述符简化了对新测序基因组的基因注释。源自 OrthoDB 的通用单拷贝直系同源物 （BUSCO） 的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，具有评估真核和原核物种的独特能力。它适用于基因集、转录组、基因组组装和宏基因组 bin。