IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP


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
(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...).

P.S.: More help by mail, if needed
Francois Jeanmougin
Service de bioinformatique / bioinformatics service
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)

More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net