[Biojava-l] Regarding problen in Alignment

[Andreas Dräger]

Dear Anant Jain,

Sorry for this misunderstanding. There is no substitution matrix 
"PROTEIN_TERM". The constructor of the BioJava SubstitutionMatrix class 
requires the following arguments: FiniteAlphabet alpha and File 
matrixFile. As the alphabet you should use the alphabet "PROTEIN_TERM" 
for matrixes of protein sequences like BLOSUM etc. In the BioJava 
repository there is a newer version of this class that provides a 
function to parse a matrix without explicitely providing an alphabet (it 
guesses the alphabet of the matrix). I hope this helps.

Cheers
Andreas Dräger

Anant Jain wrote:
> Thank You Sir,
>                        I  have searched through ftp/...blast/matrices,
> but did not got any file substitution matrix like PROTEIN_TERM,  if u
> have can u send me it OR tell me link from where i can download the it
> 
> Thank You
> Anant jain
> DYPBI
> Pune, India.
>