ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool - PubMed (original) (raw)

. 2010 Jul;38(Web Server issue):W462-8.

doi: 10.1093/nar/gkq319. Epub 2010 Apr 30.

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ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool

Jeffry D Sander et al. Nucleic Acids Res. 2010 Jul.

Abstract

ZiFiT (Zinc Finger Targeter) is a simple and intuitive web-based tool that provides an interface to identify potential binding sites for engineered zinc finger proteins (ZFPs) in user-supplied DNA sequences. In this updated version, ZiFiT identifies potential sites for ZFPs made by both the modular assembly and OPEN engineering methods. In addition, ZiFiT now integrates additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database (ZiFDB) of engineered ZFPs, and direct querying of NCBI BLAST servers for identifying potential off-target sites within a host genome. Taken together, these features facilitate design of ZFPs using reagents made available to the academic research community by the Zinc Finger Consortium. ZiFiT is freely available on the web without registration at http://bindr.gdcb.iastate.edu/ZiFiT/.

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Figures

Figure 1.

Figure 1.

ZiFiT Input Window. In this example the user has chosen to scan for ZFN sites using OPEN. The sequence has been entered in FASTA format, with exon sequences in uppercase and intron sequences in lowercase. Published sets of OPEN finger pools available through the Zinc Finger Consortium are checked by default.

Figure 2.

Figure 2.

ZiFiT Output Windows. (A) The Graphic Summary window (top) displays potential ZFN-binding sites (‘hits’) identified in the input sequence. Exons (denoted by uppercase characters in the input sequence) are displayed as thick red bars and introns as thin red lines. Hits are represented by short colored bars above the input sequence track; these serve as bookmarks that are linked to individual target sites in the Detailed Target List. ZFN hits are color-coded based on spacer size (5 bp = Blue; 6 bp = Green; 7 bp = Gold). (B) The Detailed Target List window (bottom) provides in-depth information about each hit. Hits are presented as double-stranded DNA sequences and labeled according to the FASTA description, spacer size, and index. Each hit can be expanded to reveal a reagent list for generating the corresponding ZFP. Hits can be sorted according to various criteria as detailed in the text.

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