How to emulate Blast’s “Short Sequence Parameters”

Monday October 27, 2008 • Leave a Comment 

I just spent an hour figuring out how to emulate Blast’s “Short Sequence Search Parameters” in BioPython 1.48.   To use PAM30 as your matrix you must use existence and extension parameters (e.g. gap costs) of 9 and 1.

Here’s what I’ve currently got:

result_handle = NCBIWWW.qblast(

"blastp",

"nr",

seq_record.seq.tostring(),

matrix_name = 'BLOSUM62',

word_size='2',

expect='30000',

gapcosts ='9 1',

composition_based_statistics='no adjustment')