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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse

Kim D Pruitt¹, Jennifer Harrow, Rachel A Harte

¹National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA. Pruitt@ncbi.nlm.nih.gov

Genome Research

|June 6, 2009

Summary

This summary is machine-generated.

The Consensus Coding Sequence project ensures reliable gene and protein identification across major genome browsers for human and mouse. This collaborative effort provides a high-confidence, consistently annotated protein-coding set, improving genomic research accuracy.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Accurate gene and protein identification is crucial for understanding human and mouse genomes.
Discrepancies in annotation methods across public resources hinder consistent genomic data interpretation.
The need for a unified, reliable annotation set for protein-coding regions is evident.

Purpose of the Study:

To establish and maintain a consensus set of protein-coding regions for human and mouse reference genomes.
To ensure consistent and reliable protein annotation across major genome browsers (NCBI, Ensembl, UCSC).
To provide a stable identifier (CCDS ID) for identical protein annotations.

Main Methods:

Collaborative manual review of protein annotations across contributing sites.
Coordination to resolve inconsistencies and incorporate new evidence for annotation refinement.
Tracking of identical protein-coding sequences on reference human and mouse genomes.

Main Results:

The Consensus Coding Sequence (CCDS) project has identified 20,159 human and 17,707 mouse consensus coding regions.
These regions originate from 17,052 human and 16,893 mouse genes, ensuring comprehensive coverage.
Evaluation methods confirm that CCDS entries are highly likely to represent authentic proteins, surpassing non-CCDS annotations.

Conclusions:

The CCDS project successfully centralizes the identification of well-supported, identically annotated protein-coding regions.
This consensus set enhances the reliability and biological accuracy of genomic annotations for human and mouse.
CCDS provides a vital resource for researchers, facilitating effective use of genomic data.