Zinc Finger Targeter (ZiFiT) is a simple and intuitive web-based tool that facilitates the design of zinc finger proteins (ZFPs) that can bind to specific DNA sequences. The current version of ZiFiT is based on a widely employed method of ZFP design, the 'modular assembly' approach, in which pre-existing individual zinc fingers are linked together to recognize desired target DNA sequences. Several research groups have described experimentally characterized zinc finger modules that bind many of the 64 possible DNA triplets. ZiFiT leverages the combined capabilities of three of the largest and best characterized module archives by enabling users to select fingers from any of these sets. ZiFiT searches a query DNA sequence for target sites for which a ZFP can be designed using modules available in one or more of the three archives. In addition, ZiFiT output facilitates identification of specific zinc finger modules that are publicly available from the Zinc Finger Consortium. ZiFiT is freely available at http://bindr.gdcb.iastate. edu/ZiFiT/.
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We respectfully acknowledge those who have shared their results with the zinc finger research community. We also thank users and referees for providing many helpful suggestions that have improved the ZiFiT server. This work is supported in part by NIH grant GM066387 (D.D) & NSF grant DBI 0501678 (D.F.V.) and graduate research assistantships provided by USDA MGET grant 2001-52100-11506 and ISU Center for Integrated Animal Genomics (CIAG). J.K.J is supported by NIH grants GM0699006 and GM072621. Funding to pay the Open Access publication charges for this article was provided by NFS Grant DBI 0501678.