An environmental signature for 323 microbial genomes based on codon adaptation indices.

ABSTRACT:

Background

Codon adaptation indices (CAIs) represent an evolutionary strategy to modulate gene expression and have widely been used to predict potentially highly expressed genes within microbial genomes. Here, we evaluate and compare two very different methods for estimating CAI values, one corresponding to translational codon usage bias and the second obtained mathematically by searching for the most dominant codon bias.

Results

The level of correlation between these two CAI methods is a simple and intuitive measure of the degree of translational bias in an organism, and from this we confirm that fast replicating bacteria are more likely to have a dominant translational codon usage bias than are slow replicating bacteria, and that this translational codon usage bias may be

SUBMITTER: Willenbrock H 

PROVIDER: S-EPMC1794427 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature