profile-3D sequence search

Arne Elofsson arne at rune.biokemi.su.se
Tue Jan 2 11:50:36 EST 1996


In article <Pine.SOL.3.91.951228181433.9248A-100000 at gate> ccchuang at GATE.SINICA.EDU.TW (Chyh-chong Chuang) writes:

> 
> 
> Dear Sir:
> 
> 	By  insightII's profile 3D modual, I created a profile file of a 
> sequence with known 3D structure. Is it possible to do a structural 
> compability sequence search of some database, like SwissPort, EMBL ..., 
> base on the insightII's profile file.



> 	GCG support a profile search (profilesearch command) base on a 
> sequence's profile file. It seems that the GCG's profile is not 
> calculate from a know 3D structure and sequence.   
> 	
The profile in gcg is created multiple sequence alignments (gribskov
et al 198?) while the insight 3d-1d profiles are made from structure
information (bowie et al 1991). The program to create 3d-1d profiles
can be obtained (for free) from ling at ewald.mbi.ucla.edu. Both profiles
can be used in the profilescan and profilesearch programs in gcg.


arne


(To think before you speak is as to wipe your ass before you defecate.)
-----------------------------------------------------------------
      From: Arne Elofsson           Email: arne at biokemi.su.se
      Tel:+46(0)8-161553   WWW:  http://rune.biokemi.su.se/~arne/



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