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Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design
Aikaterini Alexaki1, Jacob Kames1, David D Holcomb1
1Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
Journal of Molecular Biology
|April 29, 2019
Summary
Codon-pair bias, distinct from codon usage bias, impacts gene translation and is species-specific. A new database provides essential codon-pair usage data for researchers, aiding genetic engineering and disease studies.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Sequential codon-pair usage is non-random and unique to each species.
- Codon-pair bias influences translational fidelity and efficiency, potentially impacting human diseases.
- Existing codon-pair usage data is not readily available, hindering research.
Purpose of the Study:
- To systematically address the lack of readily available codon-pair usage data.
- To construct a comprehensive database of genomic codon-pair and dinucleotide statistics.
- To provide a valuable resource for researchers in academia and the pharmaceutical industry.
Main Methods:
- Utilized existing HIVE-Codon Usage Tables.
- Constructed a new database incorporating genomic codon-pair and dinucleotide statistics.
- Included data for all organisms with sequenced genomes available in GenBank.
Main Results:
- Developed a computational resource providing systematic codon-pair usage data.
- The database includes genomic codon-pair and dinucleotide statistics for numerous organisms.
- The resource is accessible at https://hive.biochemistry.gwu.edu/review/codon2.
Conclusions:
- The new database addresses the critical need for codon-pair usage information.
- This resource is expected to be invaluable for understanding gene translation and its implications.
- Facilitates advancements in recombinant gene technologies and disease research.
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