Relative Codon Deoptimization Index / Expected RCDI

The RCDI server is a web-application that calculates the Relative Codon Deoptimization Index (RCDI) and an expected value of the RCDI for a set of query sequences by generating random sequences with similar G+C content and amino acid composition to the input. This expected RCDI therefore provides a direct threshold value for discerning whether the differences in the RCDI value are statistically significant and arise from the codon preferences or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences. Please, click here to get a quick tutorial.

HOW TO CITE: Puigbo P, Aragones L and Garcia-Vallve S. (2010) RCDI/eRCDI: a web-server to estimate codon usage deoptimization. BMC Research Notes,3:87.

Click here to see an example

Insert your sequences in FASTA format help

Insert codon usage table (codon usage database format) help

Insert %G+C content (Optional) help

Upper (one-side) tolerance limit help


Choose the method help

Length of random sequences
Please, freely download the local version if more accurate analysis is required

Choose genetic code help

Click here to see an example

For comments, suggestions or questions please send an e-mail to Pere Puigbo (puigboap AT ncbi.nlm.nih.gov) . Please put 'RCDI' as a subject.