TRANSFAC 3.2

Thomas Heinemeyer THH at GBF-Braunschweig.DE
Mon Jun 30 11:56:02 EST 1997


*************************************************************

       T R A N S F A C  3.2   is available now at:

                 http://transfac.gbf.de/

   On the TRANSFAC server, you will find also the sequence
                    analysis programs

                     PatSearch
                     MatInspector
                     SaGa

and Thure Etzold's SRS5 with a large collection of databases.

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TRANSFAC is a database about eukaryotic transcription factors
and their binding sites.

It consists of six cross-linked tables:

        SITE
        CELL
        FACTOR
        CLASS
        MATRIX
        GENE

It is also cross-linked  with TRRD (Transcription Regulatory
Region Database) and COMPEL from the ICG, Novosibirsk (N. A.
Kolchanov, A. E. Kel). It contains numerous cross-references
to external  databases  such  EMBL, SWISSPROT, PIR, FLYBASE,
EPD, and PROSITE.  For further details see Wingender et al.,
Nucleic Acids Res. 25:265-268, 1997.

NEW FEATURES are:
-      Additional FACTOR and SITE entries,
-      cross-references to PDB,
-      comprehensive  linkage  of  FACTOR  entries with a
       proposed transcription factor classification sytem
       (http://transfac.gbf.de/TRANSFAC/cl/cl.html).

The TRANSFAC  database  comes  along  with  several sequence
analysis tools such as
-      PatSearch, which uses the sequence information
       contained in the SITE table for analysis of
       submitted sequences,
-      MatInspector, using a library of matrices selected
       from the TRANSFAC MATRIX table (see Quandt et al.,
       Nucleic Acids Res. 23:4878-4884, 1995).

Moreover, the TRANSFAC  server provides a new program (SaGa:
structural analysis  with  genetic  algorithms, developed by
Stefan Meier)  which  can  be  used  to  identify structural
characteristics  in  the  environment  of aligned functional
sites, e.g., transcription factor binding sites. SaGa uses a
library of structural parameters developed by H. Sklenar and
coworkers (MDC, Berlin; see Karas et al., CABIOS 12:441-446,
1996).

The SRS5 system ( http://transfac.gbf.de/srs5/ ) implemented
on the TRANSFAC server comprises the following databases, in
addition to the TRANSFAC tables:

        EMBL, EMBLNEW
        SWISSPROT, SWISSNEW
        TREMBL
        SPTREMBL
        REMTREMBL
        PIR
        EPD
        PDB
        PROSITE
        ENZYME

EMBLNEW is now updated daily from the European Bioinformatics
Institute (EBI) in Hinxton.


Edgar Wingender
Thomas Heinemeyer

-------------------------------------------------------------
Dr. Edgar Wingender             Tel.:   ++49(0)531 6181 426
Ges. f. Biotechn. Forsch. mbH   Fax:    ++49(0)531 6181 266
Abt. Genomanalyse               E-Mail: ewi at gbf.de
Mascheroder Weg 1               http://transfac.gbf.de/Staff/ewi.html
D-38124 Braunschweig

Dr. Thomas Heinemeyer           Tel.:   ++49(0)531 6181 295
Ges. f. Biotechn. Forsch. mbH   Fax:    ++49(0)531 6181 266
Abt. Genomanalyse               E-Mail: thh at gbf.de
Mascheroder Weg 1               http://transfac.gbf.de/Staff/thh.html
D-38124 Braunschweig





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