RCDI/eRCDI: A web-server to estimate codon usage deoptimization

被引：54
|
作者：
Puigbò P. [1 ]
Aragonès L. [2 ]
Garcia-Vallvé S. [3 ]
机构：
[1] National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
[2] Department of Microbiology, University of Barcelona
[3] Department of Biochemistry and Biotechnology, Nutrigenomics Research Group, Rovira i Virgili University
来源：
BMC Research Notes | / 3卷 / 1期
基金：
美国国家卫生研究院;
关键词：
Codon; Reference Genome; Amino Acid Composition; Codon Usage; Test Sequence;
D O I：
10.1186/1756-0500-3-87
中图分类号：
学科分类号：
摘要：
Background. The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome. Findings. RCDI/eRCDI is a web application server that calculates the Relative Codon Deoptimization Index and a new expected value for the RCDI (eRCDI). The RCDI is used to estimate the similarity of the codon frequencies of a specific gene in comparison to a given reference genome. The eRCDI is determined by generating random sequences with similar G+C and amino acid composition to the input sequences and may be used as an indicator of the significance of the RCDI values. RCDI/eRCDI is freely available at http://genomes.urv.cat/CAIcal/RCDI. Conclusions. This web server will be a useful tool for genome analysis, to understand host-virus phylogenetic relationships or to infer the potential host range of a virus and its replication strategy, as well as in experimental virology to ease the step of gene design for heterologous protein expression. © 2010 Puigb et al; licensee BioMed Central Ltd.
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