[Biojava-l] Regarding problen in Alignment

[Andreas Dräger]

Anant Jain wrote:
> Thank Sir,
>                 
> So should i use this
>  
> SubstituionMatrix matrix = new SubstitutionMatrix("PROTEIN_TERM",new 
> File (BLOSUM62.50"));
>  
>  
> Anant Jain
> DYPBBI,
> Pune,India

Dear Anant Jain,


"PROTEIN_TERM" is a String and not a FiniteAlphabet. Please have a look 
at the following example, where the alphabet "DNA" is used. Just replace 
"DNA" by "PROTEIN_TERM" and it will work for you:
http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2

Cheers
Andreas