[Biojava-l] problem in alignment

[Andreas Dräger]

Dear Anant Jain,

>                        i am aligning two protein sequences using BLOSUM62
> substitution matrix but an runtime error is coming which is " this
> tokenization does not contain character ' * ' " some IllegalSymbolException
> 
> please suggest me solution or any substitution matrix
> 
> or do i have to change my sequence format.

This problem occurs very frequently because in BioJava the * symbol (the 
termination symbol) belongs to the alphabet PROTEIN_TERM and not to the 
alphabet PROTEIN. Please use the correct alphabet and you'll be fine.

Cheers
Andreas