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valines

Keith Elliston keith_elliston at merck.com
Mon May 23 15:28:47 EST 1994


> In article <2rm5m8$cef at senator-bedfellow.MIT.EDU>, lluis at aaRS.mit.edu
> (Lluis Ribas) wrote:
> 
> >   Is there someone that can give me a clue about the following
> >   search :
> > 
> >    I need proteins of less than 50 residues without any valines
> >    in their sequences.
> >   
> >     How would you go about searching the databases for them  ?

And Conrad Halling replied:
> 
> I know of no way to find out this answer using GCG or Entrez.  However, I
> modified some code that searches the FastA version of GenPept and did this
> search on a Macintosh computer.
> 

Actually, using the GCG package on the vax, you can use findpatterns to answer 
the question.  Use the pattern <~V{1,49}~V> to search your favorite database.
(ie., N-term not val, followed by 1-49 residues that are not val, and the cterm)
If you want to use the sequences for some other analyses, or as a database,
use the /names option.

Later,

Keith

================================================================================
Keith O. Elliston                       |  Phone: (908)594-6099                 
Dept. of Bioinformatics                 |    Fax: (908)594-2929  
Merck Research Laboratories             |  Email: Elliston at merck.com 
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