title: Discrepancy among the synonymous codons with respect to their selection as optimal codon in bacteria.
abstract: The different triplets encoding the same amino acid, termed as synonymous codons, are not equally abundant in a genome. Factors such as G + C% and tRNA are known to influence their abundance in a genome. However, the order of the nucleotide in each codon per se might also be another factor impacting on its abundance values. Of the synonymous codons for specific amino acids, some are preferentially used in the high expression genes that are referred to as the 'optimal codons' (OCs). In this study, we compared OCs of the 18 amino acids in 221 species of bacteria. It is observed that there is amino acid specific influence for the selection of OCs. There is also influence of phylogeny in the choice of OCs for some amino acids such as Glu, Gln, Lys and Leu. The phenomenon of codon bias is also supported by the comparative studies of the abundance values of the synonymous codons with same G + C. It is likely that the order of the nucleotides in the triplet codon is also perhaps involved in the phenomenon of codon usage bias in organisms.
authors.affiliation: Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur 784028, Assam, India.
authors.forename: Siddhartha Sankar
authors.initials: SS
authors.lastname: Satapathy
authors.affiliation: Department of Statistics, Darrang College, Tezpur 784001, Assam, India.
authors.forename: Bhesh Raj
authors.initials: BR
authors.lastname: Powdel
authors.affiliation: Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur 784028, Assam, India.|Office of the Vice-Chancellor, Dibrugarh University, Dibrugarh 786004, Assam, India.
authors.forename: Alak Kumar
authors.initials: AK
authors.lastname: Buragohain
authors.affiliation: Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur 784028, Assam, India.
authors.forename: Suvendra Kumar
authors.initials: SK
authors.lastname: Ray
keywords: bacteria; codon usage bias; genome composition; high expression genes; optimal codon