Transcription factor software

Steve Thompson: VADMS genetics THOMPSON at WSUVMS1.CSC.WSU.EDU
Wed May 20 18:53:09 EST 1992


Fellow Netlanders--

In reply to a discussion on software for accessing Dr. Gosh's Transcription
Factor Database Michael Weise writes:

	{text deleted}
>
>	The TFD is available in the file  SITEDATA.GCG  (available via anon.
>ftp from  ncbi.nlm.nih.gov  in  /repository/TFD/datasets).  Feedback from tech
>
	{much stuff deleted}

>necessary to first create a  TFD.Patterns  file (with a format like that in
>GCG's  Prosite.Patterns ) and a set of  .TFdoc  files using the information
>found in  SITEDATA.GCG  (while the GCG package has a  TFsites.DAT  file, it
>doesn't contain all the information found in SITEDATA.GCG).  In creating 

	{more stuff deleted}
>   _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
> / Michael J. Weise, Ph.D.    \  Univ.of Ga. BioScience Computing Facility \
>(   weise at bscf.uga.edu         \   Dept.of Genetics  UGa, Athens  GA  30602 )
> \ _ _ _'Tis_only_me_speak'n._ _\_ _ _ _ _ _ _ (706) 542-1409_ _ _ _ _ _ _ /
>

However, when I ftp'ed SITEDATA.GCG over and compared it to our own GCG version
of TFsites.DAT I didn't recognize any differences.  VMS DIF saw these:
************
File DISK03:[THOMPSON.TXTFILES.BIONET]SITEDATA.GCG;1
    4   Dr. David Ghosh of the National Center for Biotechnology Information,
    5   National Library of Medicine, National Institutes of Health, maintains
    6   the relational database, TFD, from which the information in this file
    7   is derived.
    8   
******
File GENCOREDISK:[GCGCORE.DATA.MOREDATA]TFSITES.DAT;2
    4   This file is derived from the SITES table of TFD, a database
    5   of transcription factors maintained by Dr. David Ghosh at the
    6   National Center for Biotechnology Information, National Library
    7   of Medicine, National Institutes of Health.
    8   
************
************
File DISK03:[THOMPSON.TXTFILES.BIONET]SITEDATA.GCG;1
 1263   Nir_box                          0   CGCCATCTGC                                      0  !   InsfE         Mol Cell Biol 8: 2
 1264   Nod_box                          0   ATCCAAACAATCRATTTTACCAATC                       0  !   NodD             Genes Dev 2: 28
******
File GENCOREDISK:[GCGCORE.DATA.MOREDATA]TFSITES.DAT;2
 1263   Nir_box                          0   CGCCATCTGC                                      0  !   InsfE         Mol Cell Biol 8: 2
 1264   Nod_box                          0   ATCCAAACAATCRATTTTACCAATC                       0  !   NodD             Genes Dev 2: 28
************
************
File DISK03:[THOMPSON.TXTFILES.BIONET]SITEDATA.GCG;1
 1908   
******
File GENCOREDISK:[GCGCORE.DATA.MOREDATA]TFSITES.DAT;2
************

Number of difference sections found: 3
Number of difference records found: 6

DIFFERENCES /IGNORE=()/MERGED=1/OUTPUT=DISK03:[THOMPSON.TXTFILES.BIONET]SITES.DIF;1-
    DISK03:[THOMPSON.TXTFILES.BIONET]SITEDATA.GCG;1-
    GENCOREDISK:[GCGCORE.DATA.MOREDATA]TFSITES.DAT;2

Yet Micheal claims that TFsites.DAT doesn't have as much information as
SITEDATA.GCG.  What's going on?  Might it be that Micheal's version of
TFsites.DAT is not current?  Regardless, Thank's for the tips; we will pursue
the modifications and use MOTIFS as Micheal suggests.

							Steve Thompson
                              Steven M. Thompson
            Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
           Washington State University, Pullman, WA 99164-1224, USA
          AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                  BITnet:  THOMPSON at WSUVMS1 or STEVET at WSUVM1
                   INTERnet:  THOMPSON at wsuvms1.csc.wsu.edu






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