RCDI/eRCDI: a web-server to estimate codon usage deoptimization
<p>Abstract</p> <p>Background</p> <p>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.</p> <p...
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doaj-bc8e3677ece64caa9ac02abc98771c692020-11-25T02:51:59ZengBMCBMC Research Notes1756-05002010-03-01318710.1186/1756-0500-3-87RCDI/eRCDI: a web-server to estimate codon usage deoptimizationGarcia-Vallvé SantiagoAragonès LluísPuigbò Pere<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Findings</p> <p>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 <url>http://genomes.urv.cat/CAIcal/RCDI</url>.</p> <p>Conclusions</p> <p>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.</p> http://www.biomedcentral.com/1756-0500/3/87 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Garcia-Vallvé Santiago Aragonès Lluís Puigbò Pere |
spellingShingle |
Garcia-Vallvé Santiago Aragonès Lluís Puigbò Pere RCDI/eRCDI: a web-server to estimate codon usage deoptimization BMC Research Notes |
author_facet |
Garcia-Vallvé Santiago Aragonès Lluís Puigbò Pere |
author_sort |
Garcia-Vallvé Santiago |
title |
RCDI/eRCDI: a web-server to estimate codon usage deoptimization |
title_short |
RCDI/eRCDI: a web-server to estimate codon usage deoptimization |
title_full |
RCDI/eRCDI: a web-server to estimate codon usage deoptimization |
title_fullStr |
RCDI/eRCDI: a web-server to estimate codon usage deoptimization |
title_full_unstemmed |
RCDI/eRCDI: a web-server to estimate codon usage deoptimization |
title_sort |
rcdi/ercdi: a web-server to estimate codon usage deoptimization |
publisher |
BMC |
series |
BMC Research Notes |
issn |
1756-0500 |
publishDate |
2010-03-01 |
description |
<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Findings</p> <p>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 <url>http://genomes.urv.cat/CAIcal/RCDI</url>.</p> <p>Conclusions</p> <p>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.</p> |
url |
http://www.biomedcentral.com/1756-0500/3/87 |
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