ICodPack: a package for information-based analysis of codon usage
We have shown that genes with similar functions and/or similar expression patterns usually have similar codon usages (Najafabadi et al., 2009). This study was based on analyzing the distribution of codon usage values among different gene sets (such as genes with a particular function or genes with a particular expression profile) using an information-based approach. ICodPack is a package that should allow you to perform similar analysis on your organism of interest using different gene sets. It also provides a means for analysis of biological networks in terms of similarity of codon usages of interacting genes.
NOTE: If you are interested in analysis of biological networks to see whether genes with particular codon usages interact with each other, you may want to consider DICE instead of ICodPack. DICE is a general-purpose algorithm for identification of pairs of co-occurring features in biological networks, and can also be used for codon usage analysis in the context of a network. DICE provides more rigorous statistical analysis, is not limited to a particular model and can analyze all possible relationships among all values even between different codons, can find the associations of codon usage values and different gene features such as function, expression profile, conservation in different organisms, presence of a protein domain, etc., and, best of all, provides a rich graphical output!
Last updated on 7/27/2010 2:57:36 AM