Journal Article

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

Nuala A. O'Leary, Mathew 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, Yiming Bao, Olga Blinkova, Vyacheslav Brover, Vyacheslav Chetvernin, Jinna Choi, Eric Cox, Olga Ermolaeva, Catherine M. Farrell, Tamara Goldfarb, Tripti Gupta, Daniel Haft, Eneida Hatcher, Wratko Hlavina, Vinita S. 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 Schoch, Andrei Shkeda, Susan S. Storz, Hanzhen Sun, Francoise Thibaud-Nissen, Igor Tolstoy, Raymond E. Tully, Anjana R. Vatsan, Craig Wallin, David Webb, Wendy Wu, Melissa J. Landrum, Avi Kimchi, Tatiana Tatusova, Michael DiCuccio, Paul Kitts, Terence D. Murphy and Kim D. Pruitt

in Nucleic Acids Research

Volume 44, issue D1, pages D733-D745
Published in print January 2016 | ISSN: 0305-1048
Published online November 2015 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/gkv1189
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

More Like This

Show all results sharing these subjects:

  • Chemistry
  • Biochemistry
  • Bioinformatics and Computational Biology
  • Genetics and Genomics
  • Molecular and Cell Biology

GO

Show Summary Details

Preview

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.

Journal Article.  9919 words. 

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

Full text: subscription required

How to subscribe Recommend to my Librarian

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.