Consensus CDS Project
| Content | |
|---|---|
| Description | Convergence towards a standard set of gene annotations |
| Contact | |
| Research center |
National Center for Biotechnology Information European Bioinformatics Institute University of California, Santa Cruz Wellcome Trust Sanger Institute |
| Authors | Pruitt KD |
| Primary citation | Pruitt KD, et al (2009) |
| Release date | 2009 |
| Access | |
| Website | http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi |
| Miscellaneous | |
| Version | CCDS Release 21 |
The Consensus Coding Sequence (CCDS) Project is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies. The CCDS project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented by the National Center for Biotechnology Information (NCBI), Ensembl, and UCSC Genome Browser. The integrity of the CCDS dataset is maintained through stringent quality assurance testing and on-going manual curation.
Biological and biomedical research has come to rely on accurate and consistent annotation of genes and their products on genome assemblies. Reference annotations of genomes are available from various sources, each with their own independent goals and policies, which results in some annotation variation.
The CCDS project was established to identify a gold standard set of protein-coding gene annotations that are identically annotated on the human and mouse reference genome assemblies by the participating annotation groups. The CCDS gene sets that have been arrived at by consensus of the different partners now consist of over 18,000 human and over 20,000 mouse genes (see CCDS release history). The CCDS dataset is increasingly representing more alternative splicing events with each new release.
Participating annotation groups include:
Manual annotation is provided by:
"Consensus" is defined as protein-coding regions that agree at the start codon, stop codon, and splice junctions, and for which the prediction meets quality assurance benchmarks. A combination of manual and automated genome annotations provided by (NCBI) and Ensembl (which incorporates manual HAVANA annotations) are compared to identify annotations with matching genomic coordinates.
In order to ensure that CDSs are of high quality, multiple quality assurance (QA) tests are performed (Table 1). All tests are performed following the annotation comparison step of each CCDS build and are independent of individual annotation group QA tests performed prior to the annotation comparison.
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