Saturday, April 5, 2014

4 currently available tools for finding CRISPR off-targets

I was aware of 2 but heard about 2 more yesterday...  3 of these are web-based and 1 is a download/local install.   Of these. I've used the Zhang lab CRISPR design tool and ZiFit (see my Feb 18, 2014 post).   I have not yet tried Cas-OFFinder nor CasOT.   In alphabetical order:

1.  Cas-OFFinder
Reference: Bioinformatics. 2014 Feb 17. [Epub ahead of print]Cas-OFFinder: a fast and versatile algorithm that searches for potential off-targetsites of Cas9 RNA-guided endonucleases.   Bae S, Park J, Kim JS.

   This tool apparently allows searching with different PAM motifs that are recognized by Cas9 from species other than S. pyogenes.  Those variant Cas9's aren't widely used yet, but I imagine it's just a matter of time.

2. CasOT   (No web tool, local install only)
Reference: Bioinformatics. 2014 Jan 21. [Epub ahead of print]
CasOT: a genome-wide Cas9/gRNA off-target searching tool.  Xiao A, Cheng Z, Kong L, Zhu Z, Lin S, Gao G, Zhang B.

3.  Zhang lab (MIT) CRISPR design site

For identification of standard 23-base targets, scored by a metric that minimizes likelihood of off-target cleavage.  Also for locating paired targets for paired-nickase approach.    

4.  ZiFit
From the Zinc Finger Consortium; originally for zinc finger & TALEN target screening, adapted for CRISPR .  Allows identification of shorter targets for the truncated-target approach.

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