In article <4iq5lm$mks at mark.ucdavis.edu>, ez017400 at chip.ucdavis.edu
(Hemang Patel) wrote:
>> I have a friend who would like to search the TFD database using a query
> sequence and obtain a listing of all possible transcription factors
> binding sites. We have tried downloading the TFD .dat files from a number
> of ftp sites, but what do we do with them?
Even though it is not mentioned in the help, the TFD database is in the
GCG release in the datafile format for the restriction enzyme site
You can use it as follows:
First find the file on your system with
$ NAMES tfsites.dat
on our machine this gives:
then use this in any of the mapping programs. I find MAPPLOT is best,
though MAP and MAPSORT will work too.
$ mapplot /data=GENCOREDISK:[GCGCORE.DATA.MOREDATA]Tfsites.Dat
This will then give a graphical output of the position of all the sites it
If you do this often, you may find it easier to FETCH the datafile to your
Julian Parkhill - J.Parkhill at bham.ac.uk
CRC Laboratories, Inst. of Cancer Studies, Medical School,
University of Birmingham, Edgbaston, Birmingham, B15 2TJ, U.K.
Disclaimer: If I thought anybody gave a damn about my opinions....