[Bioperl-l] PAM30 with remoteBlast searches
William Pearson
wrp at virginia.edu
Wed Oct 17 13:30:21 UTC 2012
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
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