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Mega-scale Bioinformatics Investigation of Codon Bias in Vertebrates

Nabiyouni, Maryam
http://rave.ohiolink.edu/etdc/view?acc_num=mco1308092740

Abstract Details

2011, Master of Science in Biomedical Sciences (MSBS), University of Toledo, College of Medicine.
Although synonymous codon usage in mammals has been investigated for decades, there are still controversial interpretations of the observed results. Selectionism cannot explain the strong regularities in the codon bias, while neutralism is unable to comprehend the unusual high frequency of G or C nucleotides (~60%) in the third codon positions across all mammals. We performed a genome-wide computational analysis of synonymous codon usage with respect to local genomic GC-content, GC-content in the first and second codon positions, and overall genome length and GC-content. In this study, Codon Bias Index (CBI) is used to measure the codon bias in individual genes. The presented data is gathered from multiple available databases such as the Codon Usage Database, Animal Genome Size Database, BioGPS, and Exon/Intron Database. Our results suggest that local GC-content is a major contributor to the non-randomness of codon usage in mammals. Based on the obtained results, we propose a united hypothesis for the origin of GC-rich, GC-poor isochors and codon bias in mammals and vertebrates.
Alexei Fedorov, PhD (Committee Chair)
Robert Blumenthal, PhD (Committee Member)
Sadik Khuder, PhD (Committee Member)
James Willey, MD/PhD (Committee Member)
65 p.
Bioinformatics; Biology; Biomedical Research
Codon bias; GC composition; GC3; Vertebrates

Recommended Citations

Citations

  • Nabiyouni, M. (2011). Mega-scale Bioinformatics Investigation of Codon Bias in Vertebrates [Master's thesis, University of Toledo]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=mco1308092740

    APA Style (7th edition)

  • Nabiyouni, Maryam. Mega-scale Bioinformatics Investigation of Codon Bias in Vertebrates. 2011. University of Toledo, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=mco1308092740.

    MLA Style (8th edition)

  • Nabiyouni, Maryam. "Mega-scale Bioinformatics Investigation of Codon Bias in Vertebrates." Master's thesis, University of Toledo, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=mco1308092740

    Chicago Manual of Style (17th edition)

mco1308092740
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© 2011, all rights reserved.
This open access ETD is published by University of Toledo Health Science Campus and OhioLINK.