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GCG transcription factor binding sites

Steve Thompson: VADMS genetics THOMPSON at JAGUAR.CSC.WSU.EDU
Mon Mar 13 11:26:51 EST 1995


In <user-1203951403410001 at 146.9.4.72> user at cms.cc.wayne.edu states:

>Could anybody help me to search for consensus sequence against a
>transcription factor binding sites databank?  Your help is very much
>appreciated.

Use (in VMSese) David Gosh's Transcriptional Factor Sites database ---

$ FindPatterns/data=GenMoreData:TFSites.dat/In=Consense.Seq/Out=TFSites.Finds

Based on what you find in your sequence, search TFSites.dat for references.

There's also Bairoch's EPD (Eurkaryotic Promoter Database) available from EMBL
and other ftp sites which can be reformatted into standard GCG DB format and
searched with FastA or BLAST.

						- Steve

                              Steven M. Thompson
            Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
           Washington State University, Pullman, WA 99164-1224, USA
          AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                   INTERnet:  THOMPSON at jaguar.csc.wsu.edu




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