AbstractsBiology & Animal Science

Mega-scale Bioinformatics Investigation of Codon Bias in Vertebrates

by Maryam Nabiyouni

Institution: University of Toledo Health Science Campus
Department: College of Medicine
Degree: MSBS
Year: 2011
Keywords: Bioinformatics; Biology; Biomedical Research; Codon bias; GC composition; GC3; Vertebrates
Record ID: 1913077
Full text PDF: http://rave.ohiolink.edu/etdc/view?acc_num=mco1308092740


Although synonymous codon usage in mammals has been investigated for decades, thereare still controversial interpretations of the observed results. Selectionism cannot explainthe strong regularities in the codon bias, while neutralism is unable to comprehend theunusual high frequency of G or C nucleotides (~60%) in the third codon positions acrossall mammals. We performed a genome-wide computational analysis of synonymouscodon usage with respect to local genomic GC-content, GC-content in the first andsecond codon positions, and overall genome length and GC-content. In this study, CodonBias Index (CBI) is used to measure the codon bias in individual genes. The presenteddata is gathered from multiple available databases such as the Codon Usage Database,Animal Genome Size Database, BioGPS, and Exon/Intron Database. Our results suggestthat local GC-content is a major contributor to the non-randomness of codon usage inmammals. Based on the obtained results, we propose a united hypothesis for the originof GC-rich, GC-poor isochors and codon bias in mammals and vertebrates.