AllenChiu

We are currently using CRISPR/Cas system(like ZFN or TALEN) for targeted genetic modification in cells of interest, it generally works well, but we want to investigate the specificity of the modification, and thus need to predict and vilidate the possible off-target sites by PCR and subsequent sequencing.
The problem is there is no ideal tools for this purpose, as the only available online software is NCBI Blastn, which always end up with several unintended continuous match using part of our target site as query,whereas we need our whole target site to be  query.
So I will be very grateful if you can tell me some Algorithm parameters that will be helpful to keep the whole input sequence (in this case,our whole target site) as query.
Or it also will be very helpful if you know any other online software or local software that can do this job.
Thank you very much!

the attached img is a good example from a recent paper on CRISPR, but the author didn't mention the specific method to achive it.
http://www.nature.co...l/nbt.2507.html

Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease