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 |
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