RefSeq: an update on prokaryotic genome annotation and curation.
RefSeq: an update on prokaryotic genome annotation and curation.
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DOI：
10.1093/nar/gkx1068
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Pruitt KD
中科院分区：
文献类型：
--
作者：
Haft DH;DiCuccio M;Badretdin A;Brover V;Chetvernin V;O'Neill K;Li W;Chitsaz F;Derbyshire MK;Gonzales NR;Gwadz M;Lu F;Marchler GH;Song JS;Thanki N;Yamashita RA;Zheng C;Thibaud-Nissen F;Geer LY;Marchler-Bauer A;Pruitt KD
国家生物技术信息中心（NCBI）的参考序列（RefSeq）项目为超过95000个原核基因组提供注释，这些基因组符合序列质量，完整性和无污染标准。基因组由单个Proximity Genome Annotation Pipeline（PGAP）注释，为用户提供尽可能一致和准确的资源。最近值得注意的变化包括分层证据方案的开发，对管理注释证据源的新关注，蛋白质图谱隐马尔可夫模型（HALGOR）的添加和管理，更新管道（PGAP-4）的发布以及RefSeq原核基因组的全面重新注释。抗菌素耐药蛋白的结构注释得到了全面的发展，插入序列转座酶和硒蛋白的结构注释得到了改进，复杂结构域的构建为数百万个多结构域蛋白命名，本文引入了一种新的注释规则--BlastRules。支持性证据的持续管理以及RefSeq蛋白上改进名称的传播确保了基因组的功能注释保持最新。现在，越来越多的注释来自Hacking和其他注释规则集，这些规则本质上是可移植的，可供其他研究人员下载和重用。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) provides annotation for over 95 000 prokaryotic genomes that meet standards for sequence quality, completeness, and freedom from contamination. Genomes are annotated by a single Prokaryotic Genome Annotation Pipeline (PGAP) to provide users with a resource that is as consistent and accurate as possible. Notable recent changes include the development of a hierarchical evidence scheme, a new focus on curating annotation evidence sources, the addition and curation of protein profile hidden Markov models (HMMs), release of an updated pipeline (PGAP-4), and comprehensive re-annotation of RefSeq prokaryotic genomes. Antimicrobial resistance proteins have been reannotated comprehensively, improved structural annotation of insertion sequence transposases and selenoproteins is provided, curated complex domain architectures have given upgraded names to millions of multidomain proteins, and we introduce a new kind of annotation rule—BlastRules. Continual curation of supporting evidence, and propagation of improved names onto RefSeq proteins ensures that the functional annotation of genomes is kept current. An increasing share of our annotation now derives from HMMs and other sets of annotation rules that are portable by nature, and available for download and for reuse by other investigators. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/.
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影响因子：
14.9
作者：
Haft DH;Selengut JD;Richter RA;Harkins D;Basu MK;Beck E
通讯作者：
Beck E
影响因子：
14.9
作者：
Klimke W;Agarwala R;Badretdin A;Chetvernin S;Ciufo S;Fedorov B;Kiryutin B;O'Neill K;Resch W;Resenchuk S;Schafer S;Tolstoy I;Tatusova T
通讯作者：
Tatusova T
影响因子：
14.9
作者：
Cochrane G;Karsch-Mizrachi I;Takagi T;International Nucleotide Sequence Database Collaboration
通讯作者：
International Nucleotide Sequence Database Collaboration
影响因子：
14.9
作者：
Tatusova T;Ciufo S;Fedorov B;O'Neill K;Tolstoy I
通讯作者：
Tolstoy I
影响因子：
14.9
作者：
Haft, DH;Loftus, BJ;White, O
通讯作者：
White, O