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motiff

Francois Jeanmougin pingouin at crystal.u-strasbg.fr
Mon Oct 7 10:41:16 EST 1996


In article <532jml$ih1 at mserv1.dl.ac.uk>,
	Adrian Jenkins <ajenkins at nibsc.ac.uk> writes:
>Hi folks,
>
>Within GCG, there is the motif program which using the prosite database 
>searches for known motifs etc.
>
>Is there a similar program for searching for similartypes of motiffs but
>on DNA, in particular the NF-ATp-binding sites in cytokine-binding..

	I didn't find time to check if this pattern is in tfsites.
I think someone can remember me where to find the consensus
database tfsites ('little bit busy today...). We have it:

-----
This file is a composite from the following datasets:

TFD (release 7.4) SITES dataset file, 1/95
Transfac (release 2.2) SITES dataset selected entries, 12/94

References:     Nucleic Acids Res 21, 3117-8 (1993).
                J Biotechnol 35, 273-380 (1994).
                In Gene Transcription: A Practical Approach, 321-45 (1993)


Note that some entries in this file are prefixed by ;. These entries
have recognition sites which are very common and therefore by default
these entries are not included in the search (according to David Ghosh these
are entries for which N_PROB > 5.0e-04). If you wish your search
to include these entries, specify /ENZ=** (VMS) or -enz=** (UNIX) on
the command line of any of the mapping programs (MAP, MAPLOT, or
MAPSORT).
(continuing with sites...)
-----

	You can use such file or create one with your own sites.
Then use findpatterns with the good option (-dat) to call the file.
finpatterns can search a database (Oh, sorry, have a look at EGCG
because of limitation in number of sequences, it's not enough
for genbank...).

						Francois.
P.S.: More help by mail, if needed
-- 
Francois Jeanmougin
Service de bioinformatique / bioinformatics service
IGBMC BP 163
67404 Illkirch France
tel : (33) 88 65 32 71
e-mail : jeanmougin at igbmc.u-strasbg.fr
"Tout ca m'est tergal, qu'il laine ou qu'il chandail" (STTELLLA)




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