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RCDI/eRCDI: a web-server to estimate codon usage deoptimization.
Pere Puigbò1, Lluís Aragonès, Santiago Garcia-Vallvé
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. puigboap@ncbi.nlm.nih.gov.
BMC Research Notes
|April 2, 2010
Summary
The Relative Codon Deoptimization Index (RCDI) tool assesses gene codon usage similarity to reference genomes. This web application also introduces an expected RCDI (eRCDI) for significance analysis, aiding genome and virology research.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- The Relative Codon Deoptimization Index (RCDI) quantifies codon usage bias.
- RCDI compares a gene's codon usage against a reference genome's codon usage.
Purpose of the Study:
- Introduce the RCDI/eRCDI web application.
- Provide a tool for calculating RCDI and a new expected RCDI (eRCDI).
- Facilitate genome analysis and gene design.
Main Methods:
- The RCDI/eRCDI web server calculates the Relative Codon Deoptimization Index.
- It computes an expected RCDI (eRCDI) using random sequences with similar composition.
- Compares gene codon frequencies to a reference genome.
Main Results:
- The RCDI/eRCDI web application is now available.
- It provides RCDI values and a novel eRCDI metric.
- eRCDI serves as a significance indicator for RCDI values.
Conclusions:
- The RCDI/eRCDI web server is a valuable tool for genome analysis.
- It aids in understanding host-virus relationships and viral host range.
- Facilitates gene design for heterologous protein expression in experimental virology.
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