Please help me out whether I can use my modified matrix with the standalone BLAST program or PSIBLAST program. If "YES" then how?
Thanks in advance :)
Give blast the option matrix name.of.your.matrix
Thanks for answering. But i dont wanna give already existing matrices. It is allowing for its existing ones not the one i created i.e. BLOSUM_MOD.
here is the error:
BLAST query/options error: BLOSUM_MOD is not a supported matrix, supported matrices are:
Seems like NCBI BLAST doesn't support it, but WU-BLAST might: What Substitution Matrices Are Available For Blast?
There is a dirty hack on NCBI blast A: Custom Matrices With Ncbi Blast