[EMBOSS] question using 'matpatmotifs' - Checked by AntiVir DEMO ve

[Guy Bottu]

On Thu, Jan 18, 2007 at 09:14:20AM -0500, Jean Mao wrote:
> I used 'swissprot:hair_drome' as input sequence and run 'matpatmotifs' in
> EMBOSS and got 0 hits. However, when I used the same input sequnce on
> interproscan, the result
> (http://www.ebi.ac.uk/cgi-bin/iprscan/iprscan?tool=iprscan&jobid=iprscan-200
> 70118-14025926) show that it contains basic Helix-loop-helix motif which is
> ID PS50888 in prosite database. Is this a bug or did I do something wrong? I
> also run the same sequence against the 'motifs' program in GCG package.
> Again no hit was found. 

The reason is that GCG motifs and EMBOSS patmatmotif search only the 
PROSITE entries of type "pattern", while PS50888 is of type "matrix". If 
you want to search the complete PROSITE (patterns+matrices+rules), you can 
download the ps_scan script from ftp://ftp.expasy.org/databases/prosite/tools/ps_scan/sources
and the pftools package from 
ftp://ftp.isrec.isb-sib.ch/pub/sib-isrec/pftools/pft2.3
You can run this under EMBOSS with the wrappers4EMBOSS package 
(http://wemboss.sourceforge.net/).

	Hope this helps,
	Guy Bottu,
	BEN