how to find transcription factor binding sites in a sequence? - (Jun/01/2005 )

Does anyone have a good website or tool for transcription factor searching?
Thanks a lot

-hewenjuan-

You can search Transfac at http://www.gene-regulation.com/pub/databases.html (requires registration)

TFsearch
http://www.cbrc.jp/research/db/TFSEARCH.html

-sage-

thx
but the TFsearch website doesn't work well.
Sometimes it works, sometimes it doesn't work. I mean if you paste the sequence and click on Exec, on response at all

-hewenjuan-

QUOTE (hewenjuan @ Jun 2 2005, 09:45 AM)

thx
but the TFsearch website doesn't work well.
Sometimes it works, sometimes it doesn't work. I mean if you paste the sequence and click on Exec, on response at all

You need to input a label of your sequence, and then you need to input threshhold.

You can also try TESS at http://www.cbil.upenn.edu/cgi-bin/tess/tess33?RQ=WELCOME

I would recommend TRANSFAC > TESS > TFSEARCH. TFSEARCH use a matrix at lower version, probably 3.3. TESS is not latest, TRANSFAC is latest but need subscription.

-cyberpostdoc-

QUOTE (cyberpostdoc @ Jun 3 2005, 12:20 AM)

QUOTE (hewenjuan @ Jun 2 2005, 09:45 AM)

thx
but the TFsearch website doesn't work well.
Sometimes it works, sometimes it doesn't work. I mean if you paste the sequence and click on Exec, on response at all

hi
if the TF search is not working properly then u give the DNA sequene without numbering ..it will work properly.

-ruchita_sweet-