Amino acid usage is asymmetrically biased in AT- and GC-rich microbial genomes.

ABSTRACT:

Introduction

Genomic base composition ranges from less than 25% AT to more than 85% AT in prokaryotes. Since only a small fraction of prokaryotic genomes is not protein coding even a minor change in genomic base composition will induce profound protein changes. We examined how amino acid and codon frequencies were distributed in over 2000 microbial genomes and how these distributions were affected by base compositional changes. In addition, we wanted to know how genome-wide amino acid usage was biased in the different genomes and how changes to base composition and mutations affected this bias. To carry this out, we used a Generalized Additive Mixed-effects Model (GAMM) to explore non-linear associations and strong data dependences in closely related microbes; principal component a

SUBMITTER: Bohlin J 

PROVIDER: S-EPMC3724673 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature