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

By Wenjun Li, Kathleen O'Neill, Daniel H. Haft, Michael DiCuccio, Vyacheslav Chetvernin, Azat Badretdin, George F. Coulouris, Farideh Chitsaz, Myra K. Derbyshire, A. S. Durkin and 11 more. Nucleic Acids Res., 2020

960 citations recorded by the source corpus.

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/.

Subfields: Molecular Biology

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Citations in the corpus

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy (2021, background): “This is the sixth release (i.e. R06) of the GTDB since its inception in November 2017 and comprises genomes in the NCBI Assembly database as of September 2020, i.e. the release date of RefSeq 202 (14).”
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences (2021, background): “Application on empirical data To test KaKs_Calculator 3.0, we choose three empirical lncRNA genes that are extensively studied according to LncRNAWiki [7] and collect their human-mouse orthologs as well as their adjacent coding orthologs from NGDC LncBook [31] and NCBI RefSeq [32].”
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest (2022, methodology): “For this, STRING automatically recognizes several formats of FASTA headers including those from RefSeq (57), UniProtKB (54) and Ensembl (53), and checks for any apparent errors such as duplicate sequence identifiers.”
InterPro in 2022 (2022, neutral): “NCBIFAMs is currently in release 10 (https://ftp.ncbi.nlm.nih.gov/hmm/10.0/).”
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification (2021, methodology): “Protein products and gene symbols are extracted from RefSeq non- redundant protein records [16], UniProt/SwissProt [17], AMRFinderPlus [33] or ISfinder [37].”