title: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.
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.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Nuala A
authors.initials: NA
authors.lastname: O'Leary
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Mathew W
authors.initials: MW
authors.lastname: Wright
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: J Rodney
authors.initials: JR
authors.lastname: Brister
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Stacy
authors.initials: S
authors.lastname: Ciufo
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Diana
authors.initials: D
authors.lastname: Haddad
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Rich
authors.initials: R
authors.lastname: McVeigh
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Bhanu
authors.initials: B
authors.lastname: Rajput
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Barbara
authors.initials: B
authors.lastname: Robbertse
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Smith-White
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Danso
authors.initials: D
authors.lastname: Ako-Adjei
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Astashyn
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Azat
authors.initials: A
authors.lastname: Badretdin
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Yiming
authors.initials: Y
authors.lastname: Bao
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Olga
authors.initials: O
authors.lastname: Blinkova
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Vyacheslav
authors.initials: V
authors.lastname: Brover
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Vyacheslav
authors.initials: V
authors.lastname: Chetvernin
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Jinna
authors.initials: J
authors.lastname: Choi
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Cox
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Olga
authors.initials: O
authors.lastname: Ermolaeva
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Farrell
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Tamara
authors.initials: T
authors.lastname: Goldfarb
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Tripti
authors.initials: T
authors.lastname: Gupta
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Haft
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Eneida
authors.initials: E
authors.lastname: Hatcher
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Wratko
authors.initials: W
authors.lastname: Hlavina
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Vinita S
authors.initials: VS
authors.lastname: Joardar
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Vamsi K
authors.initials: VK
authors.lastname: Kodali
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Li
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Donna
authors.initials: D
authors.lastname: Maglott
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Masterson
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Kelly M
authors.initials: KM
authors.lastname: McGarvey
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Murphy
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Kathleen
authors.initials: K
authors.lastname: O'Neill
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Shashikant
authors.initials: S
authors.lastname: Pujar
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Sanjida H
authors.initials: SH
authors.lastname: Rangwala
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Rausch
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Lillian D
authors.initials: LD
authors.lastname: Riddick
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Conrad
authors.initials: C
authors.lastname: Schoch
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Andrei
authors.initials: A
authors.lastname: Shkeda
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Susan S
authors.initials: SS
authors.lastname: Storz
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Hanzhen
authors.initials: H
authors.lastname: Sun
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Francoise
authors.initials: F
authors.lastname: Thibaud-Nissen
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Igor
authors.initials: I
authors.lastname: Tolstoy
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Raymond E
authors.initials: RE
authors.lastname: Tully
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Anjana R
authors.initials: AR
authors.lastname: Vatsan
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Craig
authors.initials: C
authors.lastname: Wallin
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: David
authors.initials: D
authors.lastname: Webb
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Wendy
authors.initials: W
authors.lastname: Wu
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Landrum
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Avi
authors.initials: A
authors.lastname: Kimchi
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Tatusova
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: DiCuccio
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Kitts
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Terence D
authors.initials: TD
authors.lastname: Murphy
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA pruitt@ncbi.nlm.nih.gov.
authors.forename: Kim D
authors.initials: KD
authors.lastname: Pruitt
mesh_terms: D000818:Animals; D002417:Cattle; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D016681:Genome, Fungal; D015894:Genome, Human; D064349:Genome, Microbial; D018745:Genome, Plant; D016679:Genome, Viral; D023281:Genomics / Q000592:standards; D006801:Humans; D007448:Invertebrates / Q000235:genetics; D051379:Mice; D058977:Molecular Sequence Annotation; D009348:Nematoda / Q000235:genetics; D010802:Phylogeny; D062085:RNA, Long Noncoding / Q000235:genetics; D051381:Rats; D012015:Reference Standards; D020539:Sequence Analysis, Protein; D017423:Sequence Analysis, RNA; D014714:Vertebrates / Q000235:genetics
chemical_list: D062085:RNA, Long Noncoding