Nick Crawford » biopython http://www.ngcrawford.com Evolution and more... Wed, 09 Jun 2010 15:56:58 +0000 http://wordpress.org/?v=2.9.2 en hourly 1 How to emulate Blast’s “Short Sequence Parameters” http://www.ngcrawford.com/2008/10/27/how-to-emulate-blasts-short-sequence-parameters/ http://www.ngcrawford.com/2008/10/27/how-to-emulate-blasts-short-sequence-parameters/#comments Mon, 27 Oct 2008 20:52:29 +0000 Nick http://www.ngcrawford.com/?p=77 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:

  1.  result_handle = NCBIWWW.qblast(
  2.     "blastp",
  3.     "nr",
  4.     seq_record.seq.tostring(),
  5.     matrix_name = 'BLOSUM62',
  6.     word_size='2',
  7.     expect='30000',
  8.     gapcosts ='9 1',
  9.     composition_based_statistics='no adjustment')
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