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Literature DB >> 14708578

A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency.

Abstract

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.

Mesh：

Substances：
Amino Acids
Codon

Year: 2003 PMID： 14708578 DOI： 10.1007/s00239-003-2499-1

Source DB: PubMed Journal: J Mol Evol ISSN： 0022-2844 Impact factor: 2.395

34 in total

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12 in total

1. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.

Authors: Stephan Waack; Oliver Keller; Roman Asper; Thomas Brodag; Carsten Damm; Wolfgang Florian Fricke; Katharina Surovcik; Peter Meinicke; Rainer Merkl
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Authors: Kemin Zhou; Asaf Salamov; Alan Kuo; Andrea L Aerts; Xiangyang Kong; Igor V Grigoriev
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