Hi,
Here is the code I am using
Cheers,
Saif
public static void main(String args[])
{
String x=("prot sequence excluded");
String y=("prot sequence excluded");
try {
FiniteAlphabet alphabet
(FiniteAlphabetAlphabetManager.alphabetForName("PROTEIN");
SubstitutionMatrix matrix = new SubstitutionMatrix(alphabet, new
File("///Users/su24/BLOSUM62"));
// The above line causes the exception
SequenceAlignment aligner = new SmithWaterman(
-1,3,2,2,1,matrix);
Sequence query = ProteinTools.createProteinSequence(x, "query");
Sequence target = ProteinTools.createProteinSequence(y, "target");
aligner.pairwiseAlignment(query, target);
System.out.println("\nlocal alignment with SmithWaterman:\n" +
aligner.getAlignmentString());
}
catch (Exception exc) {
exc.printStackTrace();
}
}
}
Quoting Richard Holland <[EMAIL PROTECTED]>:
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> Hi. You need to include your complete program code in your email so that
> we can accurately diagnose the problem.
>
> cheers,
> Richard
>
> Saif Ur-Rehman wrote:
> > Dear All,
> >
> > I am having a problem using the Blosum62 matrix file from the NCBI website
> for
> > use in Smith-Waterman alignments. When I attempt to run my code reading in
> the
> > file to initialise the Substitution Matrix Object the following exception
> is
> > thrown
> >
> > "org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't
> > contain character: '*'"
> >
> >
> >
> > Thanking you in advance,
> >
> > Saif
> >
> >
> >
> >
>
--------------------------------------------------------------------------------
> > Saif Ur-Rehman
> > Research Student
> > The Centre for Evolution, Genes & Genomics (CEGG)
> > Sir Harold Mitchell Building
> > School of Biology
> > The University of St Andrews
> > St Andrews,
> > Fife
> > Scotland,UK
> >
> > ------------------------------------------------------------------
> > University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
> >
> > _______________________________________________
> > Biojava-l mailing list - [email protected]
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
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-------------------------------------------------------------------------------
Saif Ur-Rehman
Research Student
The Centre for Evolution, Genes & Genomics (CEGG)
Sir Harold Mitchell Building
School of Biology
The University of St Andrews
St Andrews,
Fife
Scotland,UK
------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
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