Nick Crawford » python 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 Blue Collar Bioinformatics http://www.ngcrawford.com/2009/11/22/blue-collar-bioinformatics/ http://www.ngcrawford.com/2009/11/22/blue-collar-bioinformatics/#comments Mon, 23 Nov 2009 02:02:07 +0000 Nick http://www.ngcrawford.com/?p=313 Just wanted to recommend Blue Collar Bioinformatics a slick blog with lots of useful bioinformatics scripts.  Everything is written in python and the full working source is typically available on GIT.

]]> http://www.ngcrawford.com/2009/11/22/blue-collar-bioinformatics/feed/ 0 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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