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Current status and new features of the Consensus Coding Sequence database.

Authors
  • Farrell, Catherine M1
  • O'Leary, Nuala A
  • Harte, Rachel A
  • Loveland, Jane E
  • Wilming, Laurens G
  • Wallin, Craig
  • Diekhans, Mark
  • Barrell, Daniel
  • Searle, Stephen M J
  • Aken, Bronwen
  • Hiatt, Susan M
  • Frankish, Adam
  • Suner, Marie-Marthe
  • Rajput, Bhanu
  • Steward, Charles A
  • Brown, Garth R
  • Bennett, Ruth
  • Murphy, Michael
  • Wu, Wendy
  • Kay, Mike P
  • And 23 more
  • 1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
Type
Published Article
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Publication Date
Jan 01, 2014
Volume
42
Issue
Database issue
Identifiers
DOI: 10.1093/nar/gkt1059
PMID: 24217909
Source
Medline
Language
English
License
Unknown

Abstract

The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.

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