MODIFYING BLOSUM MATRIX in PSIBLAST/BLAST

Question

[Amita]

Hi 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 :)

Answer 1

[Santosh Anand]

Give blast the option matrix name.of.your.matrix

[Amita]

Hi 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: BLOSUM80 BLOSUM62 BLOSUM50 BLOSUM45 PAM250 BLOSUM90 PAM30 PAM70

[Santosh Anand]

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