Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

TLDR

The RefSeq database at NCBI is a curated, non‑redundant collection of genomic, transcript, and protein sequences from more than 55 000 organisms, assembled from INSDC submissions through computation, manual curation, and collaboration. This paper reviews the current status of RefSeq’s viral, prokaryotic, and eukaryotic branches, details data‑access improvements, and outlines efforts to broaden taxonomic coverage and refine curation methods. The authors enhance RefSeq entries with literature, functional annotations, and nomenclature, employ RNA‑Seq and other data in manual curation, and implement functional curation initiatives for taxonomic validation, genome annotation, comparative genomics, and clinical testing.

Abstract

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.