Question: MODIFYING BLOSUM MATRIX in PSIBLAST/BLAST
0
gravatar for Amita
2.0 years ago by
Amita 0
Amita 0 wrote:

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 :)

blast psiblast blosum • 756 views
ADD COMMENTlink modified 2.0 years ago by Santosh Anand4.7k • written 2.0 years ago by Amita 0
0
gravatar for Santosh Anand
2.0 years ago by
Santosh Anand4.7k
Santosh Anand4.7k wrote:

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

ADD COMMENTlink written 2.0 years ago by Santosh Anand4.7k

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

ADD REPLYlink written 2.0 years ago by Amita 0

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

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Santosh Anand4.7k
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