ZFN

Genome-wide tag scanner for nuclease off-sites

Background: Based on the TagScan tool, this application is intended to search genomes for specific target sites and off-target sites, such as for pairs of zinc finger proteins (ZFPs), zinc finger nucleases (ZFNs) and modified homing endonucleases. This can either define a zinc finger nucleases (hetero-dimer) or allow for homo-dimers depending on the status of the checkbox in the input form.


Target Databases:
Genomes:

Search ZFN Sites:
Please Enter Left ZFN half-site 5' to 3' (min 6 nt - max 60 nt)

Please Enter Right ZFN half-site 5' to 3' (min 6 nt - max 60 nt)

Please Enter Allowed Spacing
      (one or two values separated by a comma)   
Allow Left and Right Protein Homo-Dimerization   
Number of Mismatches per half-site (max 2)     
References:

Provisional PDF: BMC Bioinformatics
ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites
Thomas J Cradick, Giovanna Ambrosini, Christian Iseli, Philipp Bucher, Anton P McCaffrey
BMC Bioinformatics 2011, 12:152 (13 May 2011)

PMID:17593978
Indexing Strategies for Rapid Searches of Short Words in Genome Sequences
Iseli C, Ambrosini G, Bucher P, and Jongeneel CV.
PLoS ONE. 2007; 2(6): e579.
Last update 3 Feb. 2010