[Bioperl-l] PAM30 with remoteBlast searches

[William Pearson]

I diagnosed the problem with BLASTP searches using PAM30.

When I copied the $request->as_string and sent it directly to the NCBI Blast server, I received the following error message:

Message ID#35 Error: Cannot validate the Blast options: Gap existence and extension values of 11 and 1 not supported for PAM30 supported values are: 32767, 32767 7, 2 6, 2 5, 2 10, 1 9, 1 8, 1

Thus, when setting:

$Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = "PAM30";

one must also adjust the gap penalties:

$Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = "9 1";

Bill Pearson