TRANSFAC 3.2 database

Dr. Dr.
Tue Jul 8 08:55:45 EST 1997


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



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