Journal article
An evaluation of measures of synonymous codon usage bias
Journal of molecular evolution, Vol.47(3), pp.268-274
09/1998
DOI: 10.1007/PL00006384
PMID: 9732453
Abstract
Synonymous codons are not generally used at equal frequencies, and this trend is observed for most genes and organisms. Several methods have been proposed and used to estimate the degree of the nonrandom use of the different synonymous codons. The estimates obtained by these methods, however, show different levels of both precision and dispersion when coding regions of a finite number of codons are under analysis. Here, we present a study, based on computer simulation, of how the different methods proposed to evaluate the nonrandom use of synonymous codons are affected by the length of the coding region analyzed. The results show that some of these methods are heavily influenced by the number of codons and that the comparison of codon usage bias between coding regions of different lengths shows a methodological bias under different conditions of nonrandom use of synonymous codons. The study of the dispersion of the estimates obtained by the different methods gives, on the other hand, an indication of the methods to be applied to compare values of codon usage bias among coding regions of equivalent length.
Details
- Title: Subtitle
- An evaluation of measures of synonymous codon usage bias
- Creators
- J M Comeron - Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, 08071 Barcelona, Spain. jcomeron@midwayM Aguadé
- Resource Type
- Journal article
- Publication Details
- Journal of molecular evolution, Vol.47(3), pp.268-274
- Publisher
- Germany
- DOI
- 10.1007/PL00006384
- PMID
- 9732453
- ISSN
- 0022-2844
- eISSN
- 1432-1432
- Language
- English
- Date published
- 09/1998
- Academic Unit
- Biology
- Record Identifier
- 9983992037202771
Metrics
46 Record Views