RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
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DOI：
10.1093/nar/gkaa1105
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发表时间：
2021-01-08
影响因子：
14.9
通讯作者：
Thibaud-Nissen, Francoise
中科院分区：
文献类型：
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作者：
Li, Wenjun;O'Neill, Kathleen R.;Thibaud-Nissen, Francoise
美国国家生物技术信息中心（NCBI）的参考序列（RefSeq）项目包含近20万个细菌和古细菌基因组以及1.5亿个蛋白质，并进行了最新注释。自2018年以来，Proximity Genome Annotation Pipeline（PGAP）的变化导致虚假注释大幅减少。PGAP用作结构和功能注释证据的蛋白质家族模型（PFMs）的分层集合扩展到超过35 000个蛋白质图谱隐马尔可夫模型（HALTH），12 300个BlastRules和36 000个策划的CDD架构。因此，超过1.22亿或79%的RefSeq蛋白质现在基于与策划的PFM的匹配而命名。基因符号、酶委员会编号或支持出版物属性在超过40%的PFMs上可用，并由它们命名的蛋白质和特征继承，促进多基因组分析和与文献的连接。遵循FAIR原则（可查找、可访问、可互操作、可重复使用），PFMs在Protein Family Models数据库中可供任何用户使用。最后，参考和代表性基因组集，RefSeq原核基因组的分类学上不同的子集，现在定期重新计算，并可用于下载和同源性搜索与BLAST。RefSeq可在https://www.ncbi.nlm.nih.gov/refseq/上找到。
The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation. Changes in the Prokaryotic Genome Annotation Pipeline (PGAP) since 2018 have resulted in a substantial reduction in spurious annotation. The hierarchical collection of protein family models (PFMs) used by PGAP as evidence for structural and functional annotation was expanded to over 35 000 protein profile hidden Markov models (HMMs), 12 300 BlastRules and 36 000 curated CDD architectures. As a result, >122 million or 79% of RefSeq proteins are now named based on a match to a curated PFM. Gene symbols, Enzyme Commission numbers or supporting publication attributes are available on over 40% of the PFMs and are inherited by the proteins and features they name, facilitating multi-genome analyses and connections to the literature. In adherence with the principles of FAIR (findable, accessible, interoperable, reusable), the PFMs are available in the Protein Family Models Entrez database to any user. Finally, the reference and representative genome set, a taxonomically diverse subset of RefSeq prokaryotic genomes, is now recalculated regularly and available for download and homology searches with BLAST. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/.