[Biojava-l] Use Of Blosum62

Saif Ur-Rehman su24 at st-andrews.ac.uk
Wed Feb 7 16:11:37 UTC 2007

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

"org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't
contain character: '*'"

Thanking you in advance,


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,

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

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