Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.
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/.
Sander
Jeffry D
JD
Department of Genetics, Development & Cell Biology; Bioinformatics & Computational Biology Program, Iowa State University, Ames, IA 50011, USA. jdsander@iastate.edu
Zaback
Peter
P
Joung
J Keith
JK
Voytas
Daniel F
DF
Dobbs
Drena
D
D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D003851:Deoxyribonucleases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D020407:Internet; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014584:User-Computer Interface; D016335:Zinc Fingers
D004268:DNA-Binding Proteins; D014157:Transcription Factors; D003851:Deoxyribonucleases