Upadhyay SK, Sharma S (2014) SSFinder: High throughput CRISPR-Cas target sites prediction tool. BioMed Research International. in press.

Clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system has been reported as a new genome editing tool. Detection of CRISPR-Cas binding site from massive genome sequence data remains challenging. Although a few methods have been reported but a high throughput computational tool/script is still not available. Here we report SSFinder a python based tool for high throughput detection of CRISPR-Cas binding site in huge nucleotide datasets.

SSFinder ready to use version is present on following link:

https://code.google.com/p/ssfinder/source/browse/SSFinder.wiki?repo=wiki

Tested results:

1. Total number of CRISPER target sites in Drosophila melanogaster chromosome X are 1058944, in which 977257 are specific for CRISPR-Cas binding.

2. Total number of CRISPER target sites in 27,416 protein coding genes of Arabidopsis thaliana (obtained from TAIR10ftp://ftp.arabidopsis.org/home/tair/Sequences/blast_datasets/TAIR10_blastsets/) are 1780846, in which 1618640 are specific for the CRISPR-Cas binding.

Regards,

Authors.