[Biojava-dev] Doing pattern matching on Proteins

[Uday Kamath]

Anyone ? anyhelp? a way to to motif search example or what am i doing wrong
below?
Thanks a ton!
Uday

On Thu, Nov 18, 2010 at 9:54 AM, Uday Kamath <kamathuday at gmail.com> wrote:

> Hello
> A simple question,
>
> In order to search a motif in Protein i used following code, is my method
> to create pattern factory right? Because matcher is going in infinite
> recurssion. Can someone suggest right usage? Thanks a ton
>
> //sample
> FiniteAlphabet alphabet = ProteinTools.getAlphabet();
> factory = PatternFactory.makeFactory(alphabet);
> SymbolList proteinSequence = ProteinTools.createProtein("CANLSTFA");
> //in the sequence find the match
> SymbolList motif = ProteinTools.createProtein("FA");
> Pattern p = HivProteaseProblem.factory.compile(
> MotifTools.createRegex(motif));
> Matcher occurences= p.matcher(proteinSequence);
>