Current status and new features of the Consensus Coding Sequence database.
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.
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.
Catherine M
CM
Farrell
Nuala A
NA
O'Leary
Rachel A
RA
Harte
Jane E
JE
Loveland
Laurens G
LG
Wilming
Craig
C
Wallin
Mark
M
Diekhans
Daniel
D
Barrell
Stephen M J
SM
Searle
Bronwen
B
Aken
Susan M
SM
Hiatt
Adam
A
Frankish
Marie-Marthe
MM
Suner
Bhanu
B
Rajput
Charles A
CA
Steward
Garth R
GR
Brown
Ruth
R
Bennett
Michael
M
Murphy
Wendy
W
Wu
Mike P
MP
Kay
Jennifer
J
Hart
Jeena
J
Rajan
Janet
J
Weber
Catherine
C
Snow
Lillian D
LD
Riddick
Toby
T
Hunt
David
D
Webb
Mark
M
Thomas
Pamela
P
Tamez
Sanjida H
SH
Rangwala
Kelly M
KM
McGarvey
Shashikant
S
Pujar
Andrei
A
Shkeda
Jonathan M
JM
Mudge
Jose M
JM
Gonzalez
James G R
JG
Gilbert
Stephen J
SJ
Trevanion
Robert
R
Baertsch
Jennifer L
JL
Harrow
Tim
T
Hubbard
James M
JM
Ostell
David
D
Haussler
Kim D
KD
Pruitt
D000818:Animals; D030541:Databases, Genetic; D005091:Exons; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D058977:Molecular Sequence Annotation; D011506:Proteins / Q000235:genetics*; D017421:Sequence Analysis
D011506:Proteins