shussain wrote:
>> Dear netters. I am looking for a website to analyse promotor DNA sequence
> for possible transcription factors binding sites. NCBI and NIH do not
> provide any resources regarding this issue. I appreciate any help in this
> matter.
1) SIGSCAN Version 4.05 suite of programs developed by Dr.Dan
Prestridge work with TRANSFAC and TFD databases
http://bimas.dcrt.nih.gov/molbio/signal/http://ch.nus.sg/gcg/sigscan/signal.htmlhttp://www.tigem.it/TIGEM/HTML/sigscan.html
2) TESS - software for locating transcription factor binding sites
in DNA sequence.(uses TRANSFAC Database )
http://agave.humgen.upenn.edu/utess/tess
3) Home of TRANSFAC - The Transcription Factor Database
and set of programs to search for TF binding sites in DNA seq.
http://transfac.gbf-braunschweig.de/TRANSFAC/index.html
4) TFSEARCH Japan
http://www.tokyo-center.genome.ad.jp/SIT/TFSEARCH.html
I'd restrain from advising which site is better/easier to use,
just be determined and prepared to spent half a day experimenting with
software options using some DNA stretch with known TF binding sites.
I personally got quite a bit of ridiculous results attempting to use
this promising services, same try for output presentation -
lots of reference links, but sometimes no DNA-binding site alignments.
You can use TRANSFAC database with the GCG software (if available) -
feel free to contact people at http://transfac.gbf-braunschweig.de/
and your system manager for database installation.
MatInspector Version 2.1 available for UNIX, DOS, Mac, Win95/NT -
check at the same place.
Good luck, Andrei.
