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
