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