A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency.
Unequal use of synonymous codons has been found in several prokaryotic and eukaryotic genomes. This bias has been associated with translational efficiency. The prevalence of this bias across lineages is currently unknown. Here, a new method (GCB) to measure codon usage bias is presented. It uses an iterative approach for the determination of codon scores and allows the computation of an index of codon bias suitable for interspecies comparison. A server to calculate GCB-values of individual genes as well as a list of compiled results are available at www.g21.bio.uni-goettingen.de. The method was applied to complete bacterial genomes. The relation of codon usage bias with amino acid composition and the choice of stop codons were determined and discussed.
Merkl
Rainer
R
Abteilung Molekulare Genetik und Präparative Molekularbiologie, Institut für Mikrobiologie und Genetik, Göttingen Genomics Laboratory, Georg-August-Universität Göttingen, Grisebachstrasse 8, D - 37077 G6ttingen, Germany. rmerkl@gwdg.de
D000596:Amino Acids / Q000235:genetics*; D001419:Bacteria / Q000235:genetics; D003062:Codon / Q000235:genetics*; D016680:Genome, Bacterial; D016681:Genome, Fungal; D008969:Molecular Sequence Data; D012441:Saccharomyces cerevisiae / Q000235:genetics; D014177:Translations
D000596:Amino Acids; D003062:Codon