Help wanted for motif search

Francois JEANMOUGIN pingouin at crystal.u-strasbg.fr
Mon Jun 2 11:13:02 EST 1997


In article <5mn7cp$l4c at net.bio.net>,
	yxl at iastate.edu (Yuxing Li) writes:
[...]
> I used program "motif"

	Well, motifs look for a protein query reagrding a bank of motifs.
If you want to use a pattern to search a protein database, you better
use findpatterns.
	If you just look for the motif in prosite, you can use SRS.

> to search for calcium-binding motifs in my local data
> file "CA.seq". But the output turned out not to be the thing I want. I don't
> know what I did wrong. Can anybody help me with this?
> 
> The local data file is as the following:
> 
> ------------------------------------------------------------------
> ..
> ca_bind_sig     1 (A,V,L,I,M,P,F,W,Y) x (S,T,N,Q,Y,D,E) x (S,T,N,Q,D,E) G
> (S,T,N,Q
> ,Y,D,E) (A,V,L,I,M,P,F,W,Y) (S,T,N,Q,Y,D,E) x x (D,E) (A,V,L,I,M,P,F,W,Y) x
> x (A
> ,V,L,I,M,P,F,W,Y) (A,V,L,I,M,P,F,W,Y) x
> ----------------------------------------------------------------------------
> After I used "motifs", there is something on my screen:
> ---------------------------------------------------------------------------
>  BIV106envaa.gcg len:        876
>  *** ERROR, SHOWFINDS cannot open "ProSiteDir:x"! ***

	Do not put spaces inside your pattern! You need spaces before and
after the 1.
	Also, in old versions of findpatterns, and probably in new ones 
(I didn't check), you need to add " 0 ! " at the end of the pattern. To see
an example of the good pattern file, just type:
	fetch pattern.dat

	Save your own file first to not overwrite.

						Hope this helps,
								Francois.
-- 
Francois Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France
e-mail : jeanmougin at igbmc.u-strasbg.fr
"C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun."(Thiefaine)




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