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TFD Database Searching

Julian Parkhill J.Parkhill at bham.ac.uk
Thu Mar 21 04:59:02 EST 1996


In article <4iq5lm$mks at mark.ucdavis.edu>, ez017400 at chip.ucdavis.edu
(Hemang Patel) wrote:

> Hello,
> 
> 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
programs.

You can use it as follows:

First find the file on your system with 

$ NAMES tfsites.dat

on our machine this gives:

GENCOREDISK:[GCGCORE.DATA.MOREDATA]

Tfsites.Dat

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
finds.

If you do this often, you may find it easier to FETCH the datafile to your
own directory.

-- 
          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....



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