An Investigation of Codon Usage Bias Including Visualization and Quantification in Organisms Exhibiting Multiple Biases

<p> Prokaryotic genomic sequence data provides a rich resource for bioinformatic analytic algorithms. Information can be extracted in many ways from the sequence data. One often overlooked process involves investigating an organism&rsquo;s codon usage. Degeneracy in the genetic code leads to multiple codons coding for the same amino acids. Organism&rsquo;s often preferentially utilize speci&filig;c codons when coding for an amino acid. This biased codon usage can be a useful trait when predicting a gene&rsquo;s expressivity or whether the gene originated from horizontal transfer. There can be multiple biases at play in a genome causing errors in the predictive process. For this reason it is important to understand the interplay of multiple biases in an organism&rsquo;s genome. We present here new techniques in the measurement and analysis of multiple biases in prokaryotic genomic data. Included is a visualization technique aimed at demonstrating genomic adherence to a set of discrete biases.</p>