Format

Send to

Choose Destination
See comment in PubMed Commons below
BMC Bioinformatics. 2012 Mar 22;13:43. doi: 10.1186/1471-2105-13-43.

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance.

Author information

1
Computational Bioscience Research Center (CBRC), King Abdullah Universitof Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.

Abstract

BACKGROUND:

Genetic mutation, selective pressure for translational efficiency and accuracy, level of gene expression, and protein function through natural selection are all believed to lead to codon usage bias (CUB). Therefore, informative measurement of CUB is of fundamental importance to making inferences regarding gene function and genome evolution. However, extant measures of CUB have not fully accounted for the quantitative effect of background nucleotide composition and have not statistically evaluated the significance of CUB in sequence analysis.

RESULTS:

Here we propose a novel measure--Codon Deviation Coefficient (CDC)--that provides an informative measurement of CUB and its statistical significance without requiring any prior knowledge. Unlike previous measures, CDC estimates CUB by accounting for background nucleotide compositions tailored to codon positions and adopts the bootstrapping to assess the statistical significance of CUB for any given sequence. We evaluate CDC by examining its effectiveness on simulated sequences and empirical data and show that CDC outperforms extant measures by achieving a more informative estimation of CUB and its statistical significance.

CONCLUSIONS:

As validated by both simulated and empirical data, CDC provides a highly informative quantification of CUB and its statistical significance, useful for determining comparative magnitudes and patterns of biased codon usage for genes or genomes with diverse sequence compositions.

PMID:
22435713
PMCID:
PMC3368730
DOI:
10.1186/1471-2105-13-43
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for BioMed Central Icon for PubMed Central
    Loading ...
    Support Center