TRANSFAC 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
FastM
and Thure Etzold's SRS5 with a large collection of databases.
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 implemented on the TRANSFAC server comprises the
following databases, in addition to the TRANSFAC tables:
EMBL, EMBLNEW
SWISSPROT, SWISSNEW
TREMBL
REMTREMBL
SPTREMBL
PIR
EPD
PDB
PROSITE
ENZYME
EMBLNEW is now updated daily on the TRANSFAC SRS-Site with the
new files from European Bioinformatics Institute (EBI) in Hinxton.
Edgar Wingender
Thomas Heinemeyer
--
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
