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repository there is a newer version of this class that provides a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.
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