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2006

P-value based visualization of codon usage data

9 years 10 months ago
P-value based visualization of codon usage data
Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by multivariate analysis of codon usage data. In particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. We here propose a multidimensional scaling approach using a novel similarity measure for codon usage tables. Our probabilistic similarity measure is based on P-values derived from the wellknown chi-square test for comparison of two distributions. Experimental results on four microbial genomes indicate that the new method is well-suited for the analysis of horizontal gene transfer and translational selection. As compared with the widely-used correspondence analysis, our method did not suffer from outlier sensitivity and showed a better clustering of putative alien genes in most cases. Background T...
Peter Meinicke, Thomas Brodag, Wolfgang Florian Fr
Added 10 Dec 2010
Updated 10 Dec 2010
Type Journal
Year 2006
Where ALMOB
Authors Peter Meinicke, Thomas Brodag, Wolfgang Florian Fricke, Stephan Waack
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