[Biojava-dev] Doing pattern matching on Proteins

[Uday Kamath]

Anyone who can answer this query? I am stuck with this in my research work,
so appreciate any response.
Uday

On Fri, Nov 19, 2010 at 1:48 PM, Uday Kamath <kamathuday at gmail.com> wrote:

>
>
> Andreas
> Thanks for your reply. I looked at it, here are the problems i faced
> 1. Matcher matcher = p.matcher(seq.seqString());
> Pattern doesn't have a method to do match on the sequence string but on the
> Sequence, atleast in my verison of BioJava
>
> 2.Pattern p = Pattern.compile( MotifTools.createRegex(motif) );
> doesnn't work so need to create a pattern factory with alphabets and
> compile it to create a pattern. So i changed the MotifLister in example to
> have
>       FiniteAlphabet alphabets = ProteinTools.getTAlphabet();
>     Pattern p = PatternFactory.makeFactory(alphabets).compile(target);
>
> 3. When i use the same code with this modification that is to do matcher()
> on sequences, it goes into recursion and throws out of memory exception.
>
> I have attached my minor modification and my input. I don't know what i am
> doing is wrong.
> JVM args were
> protein C:\Research\HIV-Protease\SampleProtein.fasta an 3
>
> Thanks for your reply, would really appreciate if you give more inkling to
> the problem
> Uday Kamath
>
>
> On Fri, Nov 19, 2010 at 12:49 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Hi Uday,
>>
>> have you seen this cookbook page?
>>
>> http://www.biojava.org/wiki/BioJava:Cookbook:Sequence:Regex
>>
>>
>> Andreas
>>
>> On Thu, Nov 18, 2010 at 7:49 PM, Uday Kamath <kamathuday at gmail.com>
>> wrote:
>> > 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);
>> >>
>> > _______________________________________________
>> > biojava-dev mailing list
>> > biojava-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> >
>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> Dr. Andreas Prlic
>> Senior Scientist, RCSB PDB Protein Data Bank
>> University of California, San Diego
>> (+1) 858.246.0526
>> -----------------------------------------------------------------------
>>
>
>
>