Hi Dear Netters,
I have some trouble in using GCG to search motif in my local data file
against my protein sequence.
I used program "motif" 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"! ***
Total finds: 399
Total length: 876
Total sequences: 1
CPU time (sec): 00.12
Output file: "/usr2/users/carpente/yuxing/BIV106envaa.motifs"
----------------------------------------------------------------------------
And the following is the output :
---------------------------------------------------------------------------
ca_bind_sig (A,V,L,I,M,P,F,W,Y)
(M)
1: M DQDLD
(L)
5: MDQD L DRAER
(A)
8: QDLDR A ERGER
(L)
20: GGSEE L LQEEI
(L)
21: GSEEL L QEEIN...
----------------------------------------------------------------------------
This result is odd. Because 1) I want longer motifs than the turnout; and 2)
The first amino acid should not include Gly but it is there. I don't know
what is going on. Can somebody point out the problem?
Thank so much for your help in advance!
Yuxing Li
--
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Yuxing Li, Post-doctoral Associate
1144 Vet. Med. Complex phone : (515)-294-9882
Iowa State University email: yxl at iastate.edu
Ames, IA 50011, USA fax : (515)-294-8500
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