[Biojava-l] Use Of Blosum62

[Saif Ur-Rehman]

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 <holland at ebi.ac.uk>:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> 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  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFFyf1y4C5LeMEKA/QRAp7zAJ9ncsgYyBBRDrgSBnANTYv0xYI+PwCgpGv0
> cQQ8vFVB8QtKW9kAt9pRSEQ=
> =2rLL
> -----END PGP SIGNATURE-----
>


-------------------------------------------------------------------------------
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