Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design
Journal of Molecular Biology
codon context; codon-pair bias; dinucleotide frequency; GenBank; gene optimization/deoptimization
© 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.
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