Current status and new features of the Consensus Coding Sequence database

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.

Figure 1.

CCDS release statistics for human and mouse. The Y-axis indicates counts of CCDS IDs or Gene IDs and the X-axis shows CCDS release dates. (A) Growth in the number of CCDS IDs at each release date (Table 1) compared with the number of Gene IDs with at least one protein isoform in the CCDS dataset. (B) Growth in the number of Gene IDs with more than one protein isoform in the CCDS dataset. All data used to generate the graphs are available in the CCDS Releases and Statistics page (http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=SHOW_STATISTICS) on the website.

Figure 2.

CCDS database screenshot showing the partial report page for CCDS59435. This CCDS ID is associated with the ‘Inferred exon combination’ attribute, as explained in the Public Note. The exon locations table is partially visible in the Chromosomal Locations section. The blue ‘N’ icon circled in red links to a graphical view of the entire genomic region in NCBI’s Nucleotide database (boxed inset image). The blue ‘N’ icons boxed in red link to the sequences of each individual exon in the Nucleotide database.