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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| Format: | Article |
| Language: | English |
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BMC
2010-03-01
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| Series: | BMC Research Notes |
| Online Access: | http://www.biomedcentral.com/1756-0500/3/87 |
| _version_ | 1828295781078007808 |
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| author | Garcia-Vallvé Santiago Aragonès Lluís Puigbò Pere |
| author_facet | Garcia-Vallvé Santiago Aragonès Lluís Puigbò Pere |
| author_sort | Garcia-Vallvé Santiago |
| collection | DOAJ |
| 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> |
| first_indexed | 2024-04-13T12:00:50Z |
| format | Article |
| id | doaj.art-bc8e3677ece64caa9ac02abc98771c69 |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-04-13T12:00:50Z |
| publishDate | 2010-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-bc8e3677ece64caa9ac02abc98771c692022-12-22T02:47:47ZengBMCBMC 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 |
| spellingShingle | Garcia-Vallvé Santiago Aragonès Lluís Puigbò Pere RCDI/eRCDI: a web-server to estimate codon usage deoptimization BMC Research Notes |
| title | 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_short | RCDI/eRCDI: a web-server to estimate codon usage deoptimization |
| title_sort | rcdi ercdi a web server to estimate codon usage deoptimization |
| url | http://www.biomedcentral.com/1756-0500/3/87 |
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