>Hello all.
>>Does anyone out there know of any software for searching the TFD database
>with a promoter sequence? In other words, I have the sequence for a
>putative promoter and would like to easily identify possible transcription
>factor binding sites in the sequence. Is there a simple way to do this without
>having to search the sequence with each binding site seperately? For example,
>could I compare my sequence with the sequences in the TFD database all at once?
>>Any help or advice would be very welcome. I have access to Unix, Mac and
>IBM computers.
>>Thanks again,
>>William M. Rideout III
>
Hello,
I) If you have access to GCG package you may use TFD with findpatterns, map,
mapplot and mapsort. (I mean the GCG version of TFD sites!)
II) The program tfd2prosite.c is available on the EMBL server. It converts
sites (or DOMAINS) table SITE.DAT (or DOMAINS.DAT) to a Prosite-like
format.
The new file (SITES.PAT or DOMAINS.PAT) can be used with Prosite-based
programs such as Macpattern (available on EMBL server.)...
To get these send the following message to NETSERV at EMBL-Heidelberg.DE :
GET MAC_SOFTWARE:TFD2PROSITE.C
GET MAC_SOFTWARE:MACPATTERN.HQX
You'll need a C compiler for tfd2prosite.c though...
Note : tfd2prosite.c and macpattern were developped at EMBL by Rainer Fuchs.
I hope this helps a little...
Frederic PLEWNIAK
LGME
11 rue Humann
67085 STRASBOURG Cedex
FRANCE
plewniak at titus.u-strasbg.fr
