RefSeq: an update on prokaryotic genome annotation and curation

By Daniel H. Haft, Michael DiCuccio, Azat Badretdin, V. Brover, Vyacheslav Chetvernin, Kathleen O'Neill, Wen J. Li, Farideh Chitsaz, Myra K. Derbyshire, Noreen R. Gonzales and 11 more. 2017

880 citations recorded by the source corpus.

Abstract 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/.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, methodology): “In order to select best representative prokaryotic genomes, we used the SpecI species delineation method (18) against a total set of 25 038 genomes retrieved from RefSeq (19), obtaining 4445 reference species.”
UniProt: the Universal Protein Knowledgebase in 2025 (2024, neutral): “We continue to expand this rule set, most recently with rules created by them based on NCBIfam signatures ( 21 ) evaluated and added to the set.”
VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses (2020, methodology): “The dataset used for benchmarking consisted of 60 T7-like phages genomes, from the Autographviridae family, downloaded from the GenBank RefSeq database [20].”
Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease (2019, neutral): “Phage genome assemblies were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) 40,41 .”
COSMIC: the Catalogue Of Somatic Mutations In Cancer (2018, background): “The first phase, which is currently underway, is to upgrade the annotation system and data model, which will facilitate still closer interoperability with external resources such as Ensembl (15), HGNC (16) and RefSeq (17), and with the increasing number of analytical and visualization systems in dev”
Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates (2019, methodology): “NCBI’s RefSeq and Prokaryotic Gene Annotation Pipeline (PGAP) now use these HMMs to perform consistent functional annotation of AMR proteins during automatic annotation of bacterial genomes (22).”
Rfam 14: expanded coverage of metagenomic, viral and microRNA families (2020, background): “Rfam and Infernal are commonly used to annotate ncRNAs in newly sequenced genomes (3,4), and are the core components of the genome annotation pipelines in Ensembl (5), Ensembl Genomes (6), NCBI Prokaryotic and Eukaryotic Gene Annotation (7,8) and other resources.”
Database resources of the National Center for Biotechnology Information. (2019, methodology): “The prokaryote dataset (7) incorporates data from over 165 000 assemblies representing over 11 000 species, primarily annotated with NCBI’s PGAP.”
The InterPro protein families and domains database: 20 years on (2020, methodology): “…database was transferred in April 2018 from the J. Craig Venter Institute (JCVI, formerly known as The Institute for Genomic Research, TIGR) to the National Center for Biotechnology Information (NCBI), where it is now actively maintained within the set of HMMs used in RefSeq annotation (22).”
CDD/SPARCLE: the conserved domain database in 2020 (2019, methodology): “An in-house version of sparclbl is part of NCBI’s prokaryotic genome annotation pipeline (PGAP) (6).”
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation (2020, background): “…records deposited in GenBank are updated only rarely, RefSeq regularly reannotates genomes with PGAP, the Prokaryotic Genome Annotation Pipeline (1,2), to reflect newly characterized prokaryotic metabolic and regulatory systems published in the literature and in specialized resources (3,4) and…”
COG database update: focus on microbial diversity, model organisms, and widespread pathogens (2020, background): “gov/2016/07/15/) and the shift of the entire database to GenBank protein accessions and non-unique RefSeq identifiers, coupled with the removal of numerous proteins from the database ((21,22), see https://www.”
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification (2021, methodology): “In a first experiment, we annotated 35 taxonomically diverse bacterial genomes from RefSeq [4].”
Information Retrieval: A Biomedical and Health Perspective (2020, background): “The second study found that in general, the rate of citation of papers correlated well with scientists’ perceived importance of the research [48].”
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities (2019, methodology): “The Kraken database used by the service is a full build that is based on all RefSeq genome sequences (47), the human genome sequence, plasmids and vector sequences.”