Crypskip is a program to analyse whether a mutated sequence favours cryptic splice site activation or exon skipping

Crypskip is a program for analysing splice site mutations. It predicts whether cryptic (non-canonical) splice site activation or exon skipping is favoured. By doing so, Crypskip searches the sequence for different sets of known splicing motives and combines the results to calculate the probability of cryptic splice site activation.

Input is a DNA sequence which contains one exon and at least 4 nucleotides of flanking intronic sequence. In addition to that the begining and ending of the exon need to be declared.

The algorithm behind Crypskip uses a combination of exonic and intronic enhancer and silencer elements to predict a so-called PCRE-value ("Probability of Cryptic Splice Site Activation"). A value higher than 0.5 indicates that cryptic splice site activation is preferred whereas a value lower than 0.5 indicates that exon skipping is favoured.

Crypskip is a re-implementation of the Crypskip web-server described in Divina, P., Kvitkovicova, A., Vorechovsky, I. (2009): Ab initio prediction of cryptic splice-site activation and exon skipping. Eur. J. Hum. Genet.

You can find Crypskip in the "Advanced Mode" of W2H both in sub-menus "Tasks" and "Gene Finding and Pattern Analysis" .

Your HUSAR team 07/07/10