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

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ID: 289403
2015
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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.
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Authors Nuala A. O’Leary, Matt W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput, Barbara Robbertse, Brian Smith-White, Danso Ako-adjei, Alexander Astashyn, Azat Badretdin, Yīmíng Bào, Olga Blinkova, Vyacheslav Brover, Vyacheslav Chetvernin, Jinna Choi, Eric Cox, Olga Ermolaeva, Catherine M. Farrell, Tamara Goldfarb, Tripti Gupta, Daniel H. Haft, Eneida Hatcher, Wratko Hlavina, Vinita Joardar, Vamsi K. Kodali, Wenjun Li, Donna Maglott, Patrick Masterson, Kelly M. McGarvey, Michael R. Murphy, Kathleen O’Neill, Shashikant Pujar, Sanjida H Rangwala, Daniel Rausch, Lillian D. Riddick, Conrad L. Schoch, Andrei Shkeda, Susan S. Storz, Hanzhen Sun, Françoise Thibaud‐Nissen, Igor Tolstoy, Raymond E. Tully, Anjana R. Vatsan, Craig Wallin, David Webb, Wendy Wu, Melissa Landrum, Avi Kimchi, Tatiana Tatusova, Michael DiCuccio, Paul Kitts, Terence D. Murphy, Kim D. Pruitt
Journal Nucleic Acids Research
Year 2015
DOI
10.1093/nar/gkv1189
URL
https://academic.oup.com/nar/article-pdf/44/D1/D733/9482930/gkv1189.pdf
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