rare codon calculator | CLARK LAB @ NOTRE DAME

Help:


Gene Sequence   ||   Codon Usage   ||   Random Reverse Translation

Gene Sequence:

(1) Must follow FASTA formatting.
(2) Each sequence must contain 3n base pairs, where n is a non-negative integer.
(3) Can submit multiple sequences as one job.
(4) Cannot exceed 25000 characters in length. If you would like to submit a larger job, please contact us.

Example:

Click here for a sample results page based on the above example sequence and ecoli codon usage.


Codon Usage:

(1) All codons must be assigned a non-negative integer.
(2) Formatting must be in "Codon Usage Database" format: [triplet] [frequency per thousand codons] ([total number in ORFeome])

Example:

OR the following format: [triplet] [number in ORFeome]

Example:


Random Reverse Translation:

The Random Reverse Translation (RRT) option creates a control with which to compare your results. Your gene sequence is translated into an amino acid sequence. This, in turn, is converted back into nucleotides according to the selected codon usage probabilities. In all, 200 RRTs are built, processed by the Rare Codon Calculator, and then averaged. It should take approximately 15 seconds to process 1000 nucleotides.


Please contact us with addition questions.

Stanley D. Strycker, web designer
an SDS webPAGE