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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by

Shashikant Pujar¹, Nuala A O'Leary¹, Catherine M Farrell¹

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Nucleic Acids Research

|November 11, 2017

Summary

The Consensus Coding Sequence (CCDS) project offers a high-quality, stable dataset of human and mouse protein-coding regions. This collaborative effort ensures accurate genome annotations through automated pipelines and expert manual review.

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Area of Science:

Genomics
Bioinformatics
Comparative Genomics

Background:

The Consensus Coding Sequence (CCDS) project is an international collaboration.
It provides a dataset of identically annotated protein-coding regions in human and mouse reference genomes.
Independent annotations from NCBI and Ensembl form the basis of the CCDS dataset.

Purpose of the Study:

To outline the ongoing work, growth, and stability of the CCDS dataset.
To provide updates on new collaboration members and features.
To highlight the importance of accurate reference genome assembly and community input.

Main Methods:

Utilizing an automated pipeline for generating identically annotated coding regions.
Implementing multiple quality assurance checks for data integrity.
Coordinated manual review by expert curators from the CCDS collaboration.

Main Results:

CCDS dataset provides stable and tracked identifiers (CCDS ID) for identically annotated coding regions.
The dataset is maintained with high integrity and quality through collaborative efforts.
CCDS data is accessible via an interactive web page and an FTP site.

Conclusions:

The CCDS project ensures high-quality, consistent genome annotations through collaboration and rigorous quality control.
Accurate reference genome assemblies and community feedback are crucial for maintaining the dataset's integrity.
The CCDS dataset continues to grow and evolve with new features and collaborators.