Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design

Authors

Aikaterini Alexaki, Food and Drug Administration
Jacob Kames, Food and Drug Administration
David D. Holcomb, Food and Drug Administration
John Athey, Food and Drug Administration
Luis V. Santana-Quintero, Food and Drug Administration
Phuc Vihn Nguyen Lam, Food and Drug Administration
Nobuko Hamasaki-Katagiri, Food and Drug Administration
Ekaterina Osipova, Food and Drug Administration
Vahan Simonyan, Food and Drug Administration
Haim Bar, University of Connecticut
Anton A. Komar, Cleveland State University
Chava Kimchi-Sarfaty, Food and Drug Administration

Document Type

Journal Article

Publication Date

6-14-2019

Journal

Journal of Molecular Biology

Volume

431

Issue

13

DOI

10.1016/j.jmb.2019.04.021

Keywords

codon context; codon-pair bias; dinucleotide frequency; GenBank; gene optimization/deoptimization

Abstract

© 2019 Usage of sequential codon-pairs is non-random and unique to each species. Codon-pair bias is related to but clearly distinct from individual codon usage bias. Codon-pair bias is thought to affect translational fidelity and efficiency and is presumed to be under the selective pressure. It was suggested that changes in codon-pair utilization may affect human disease more significantly than changes in single codons. Although recombinant gene technologies often take codon-pair usage bias into account, codon-pair usage data/tables are not readily available, thus potentially impeding research efforts. The present computational resource (https://hive.biochemistry.gwu.edu/review/codon2) systematically addresses this issue. Building on our recent HIVE-Codon Usage Tables, we constructed a new database to include genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome, available in the GenBank. We believe that the growing understanding of the importance of codon-pair usage will make this resource an invaluable tool to many researchers in academia and pharmaceutical industry.

APA Citation

Alexaki, A., Kames, J., Holcomb, D., Athey, J., Santana-Quintero, L., Lam, P., Hamasaki-Katagiri, N., Osipova, E., Simonyan, V., Bar, H., Komar, A., & Kimchi-Sarfaty, C. (2019). Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design. Journal of Molecular Biology, 431 (13). http://dx.doi.org/10.1016/j.jmb.2019.04.021