FastM 1.1: correlated TF binding sites

Kerstin Quandt quandt at no_spam.gsf.de
Tue Oct 21 04:45:47 EST 1997


We would like to announce the availability of the online version 1.1
of the programs FastM and ModelInspector, tools for detection of
correlated transcription factor binding sites in DNA sequences
(including databases).

FastM builds a so-called model from the information of
- which two binding sites are involved
      * to be selected from a library of matrix descriptions
      * or as IUPAC sequences to be provided by the user 
         (new in this release)
- their strand orientation (with respect to each other)
- and a distance range between the two binding sites.

ModelInspector then uses this FastM-model to scan either a given
DNA sequence or a selected GenBank section for matches to the model.
This allows fast verification whether a pair of binding sites is
really characteristic for the sequence you are analyzing.

You can use FastM/ModelInspector interactively via WWW at

        http://www.gsf.de/cgi-bin/fastm.pl

More information and an example can be found at

        http://www.gsf.de/biodv/fastm.html

All parameters for the programs can be set via the WWW-form,
you can select a GenBank section or enter your own sequence to be
scanned for matches.
The resulting output will be mailed to you.

The binding site library used by FastM is based on the latest release
3.2 of the TRANSFAC database
(http://transfac.gbf-braunschweig.de/TRANSFAC).

Suggestions and comments are welcome.

-- 
Kerstin Quandt                    |  email:    quandt at no_spam.gsf.de
(please remove no_spam from the email adress)
GSF - Forschungszentrum
National Research Centre for Environment and Health
85764 Neuherberg,  F.R.Germany




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