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Cited by 1,116

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

Open access
Li, Wenjun, O’Neill, Kathleen R, Haft, Daniel H, DiCuccio, Michael, Chetvernin, Vyacheslav, Badretdin, Azat, Coulouris, George, Chitsaz, Farideh, Derbyshire, Myra K, Durkin, A Scott, Gonzales, Noreen R, Gwadz, Marc, Lanczycki, Christopher J, Song, James S, Thanki, Narmada, Wang, Jiyao, Yamashita, Roxanne A, Yang, Mingzhang, Zheng, Chanjuan, Marchler-Bauer, Aron, Thibaud-Nissen, Françoise·2021·Nucleic Acids Research
DOI 10.1093/nar/gkaa1105
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Abstract

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/.

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Research works printed but not linked: 23

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Cited by

Metadata

Authors
Li, W., O’Neill, K. R., Haft, D. H., DiCuccio, M., Chetvernin, V., Badretdin, A., Coulouris, G., Chitsaz, F., Derbyshire, M. K., Durkin, A. S., Gonzales, N. R., Gwadz, M., Lanczycki, C. J., Song, J. S., Thanki, N., Wang, J., Yamashita, R. A., Yang, M., Zheng, C., Marchler-Bauer, A., & Thibaud-Nissen, F.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2020-12-03
Volume
49
Issue
D1
Pages
D1020-D1028
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkaa1105
OpenAlex
W3109735703
Cited by
1,116
References
3
FWCI
32.22
Type
journal article
Language
en
Open access
gold
Funders
National Institutes of Health

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