Transfac databases

Kornelie Frech frech at gsf.de
Fri Mar 29 04:46:42 EST 1996

Staffa at NIEHS.NIH.GOV (Nick Staffa) wrote:
>(This is my second posting using netscape mail service, since I do not 
>see my first neither on the info-gcg web page nor in my mailbox)
>I have been exploring the site 
>They maintain a database of profiles of transcription binding sites
>along with other data.  I am interested in this because I would 
>like to do a profilesearch using profiles of binding sites.
>The profiles that  Transfac gives are not acceptable to GCG.
>If I could get at the aligned sequences that were used to generate
>the profiles at Transfac, or even the raw sequences in an IG file,
>I could create my own GCG profiles with profilemake.
>Although these files are alluded to, I could not discover them after
>many hours of searching. I thought they might be included in the
>download of MatInspector,but all I found was one or two examples.
>Does anyone know how to get at the aligned sequence files used to 
>create the profiles at Transfac?

Why do want to create your own profiles? The program MatInspector does exactly
what you want. It locates matches to transcription factor binding sites in
nucleotide sequences of unlimited length. 
The GCG programs profilemake and profilesearch are developed for protein
sequence analysis. In the GCG manual is stated, that they have little
experience using nucleotide sequences with profile analysis.

MatInspector is a program that uses a large library of predefined
matrix descriptions of transcription factor binding sites
to locate matches in nucleotide sequences of unlimited length.
It assigns a quality rating to matches and thus allows a quality-
based filtering and selection of matches.
(see Quandt, K., Frech, K., Karas, H., Wingender, E., Werner, T.:
MatInd and MatInspector - New fast and versatile tools for
detection of consensus matches in nucleotide sequence data
Nucleic Acids Research 23, pp. 4878-4884 (1995)).

The library of protein binding sites contains more than 200 entries
and is based on the TRANSFAC database.

The software and the library are available for UNIX, PC and MAC at


 You can also use interactively MatInspector on the WWW at


Here the sequences to be analyzed can directly be submitted (copy and paste),
individual or groups of matrices from the library can be selected
and the resulting output can be saved for further processing.

If you have any problems in using MatInspector send an email to quandt at gsf.de.

Kornelie Frech
GSF - Forschungszentrum fuer Umwelt und Gesundheit GmbH
Institut fuer Saeugetiergenetik / AG BIODV
D - 85758 Oberschleissheim

E-mail: frech at gsf.de

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