Server at Davidson College



The Optimus
A program designed to optimize a given gene sequence


This program gives the user the option to evaluate the expression level of a sequence from ecoli using either the RCBS-PC or the CAI formula. The RCBS-PC, or Relative Codon Bias, is essential the sum of the percent error for each codon. The RCB value takes the observed codon frequency minus the expected codon frequency divided by the expected frequency (Roymondal et al, 2009).



Then to calculate RCBS you must sum up the RCB values and raise the sum to one over the number of codons (Fox . 2010).



The CAI, or Codon Adaptation Index takes the frequency of each codon in the host organism and divides it by the frequency of each codon that appears the most in the host organism; which will give wi



Then to calculate CAI you have to take the product of all the wi and raise it to 1 over L; where L equals the number of codons (Jansen et al, 2003).

The user then has the option to either optimize or deoptimize the sequence by using one of these two formulas. If the optimize or deoptimize option is selected the user will be given a new sequence in which the codons have been changed to reflect the best, or worst, codons as determined by the selected formula. However, the amino acid sequence is preserved.



Fox, Jesse M and Ivan Erill. "Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression". DNA Research 2010 May 7. pp 1-12
http://dnaresearch.oxfordjournals.org/

Jansen, Ronald et al. "Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models". Nucleic Acids Reseach 2003 v. 31 No. 8. Pp 2242-2251
http://nar.oxfordjournals.org/cgi/content/full/31/8/2242

Roymondal, Uttam et al. "Predicting Gene Expression Level from Relative Codon Usage Bias: An application to Escherichia coli Genome". DNA Reseach v. 16 2009. pp 13-30