[Bioperl-l] Script

[Jason Stajich]

You might instead try fuzzpro:
 http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/fuzzpro.html

It would be pretty trivial to write something to do what you ask with
bioperl but you might want to try and read the HOWTOs an the tutorial a
little bit before asking for people to write something for you.

For example - see how to read in sequences here:
 http://www.bioperl.org/HOWTOs/html/SeqIO.html

The you just need to know
$seq->seq() -- get the sequence as a string from the Sequence object
and the perl function index
% perldoc -f index
 to see how
the Seq object ( $seq->seq() )

An example problem here:
 http://jason.open-bio.org/~jason/Bioperl_Tutorials/Duke_2003/problem_sets/perl/02_find_subsequence.txt

With answers of course too:
 http://jason.open-bio.org/~jason/Bioperl_Tutorials/Duke_2003/problem_sets/perl/answers/


On Mon, 22 Sep 2003, Lobvi Matamoros wrote:

>
>
> Hi to everyone:
>
> I am trying to know how many times a particular amino acid motif occur in a
> protein database, for instance NCCC,  in other words count that particular
> motif. Does anyone have an script to perform that task or something close I
> can change a little bit?.
>
> Thanks for your help in advance
>
> Lobvi Matamoros Fernández, Ph.D
> Post-doctoral fellow
>
> Centre de Recherche du CHUL
> 2705 Boul. Laurier, T3-80
> Sainte-Foy (Québec)
> G1V 4G2 CANADA
> Tel: 418-6542261
> FAX:418-654-2279
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu