[Biojava-l] Use Of Blosum62

[Saif Ur-Rehman]

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



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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

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University of St Andrews Webmail: https://webmail.st-andrews.ac.uk