Nick Crawford Evolution and more…

22Nov/090

Blue Collar Bioinformatics

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.

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27Oct/080

How to emulate Blast’s “Short Sequence Parameters”

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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RSS OOE: Another blog I help write

  • From Tophat to Pysam July 21, 2010
    I recently needed to interact with a SAM file in python that was created as part of a Tophat run. Rather rolling my own parser I decided to use the handy pysam module. However, I immediately ran into trouble. I couldn’t get pysam to open my file. It turns out pysam requires a BAM file not a SAM file.  This meant I need to convert filetypes. So, I fired up sa […]
  • Inferring Heterozygosity from SNP data April 20, 2010
    This looks straightforward.  n = total number of reads aligning to a base y = total number of reads aligning to a base that match the reference p = probability that reads match the reference base Bases with LOD>3 were called SNPs or sites of heterozygosity. From Bloom et al. (2009) Measuring differential gene expression by short read sequencing: quantitat […]
  • Why we are "Python Fanboys" April 15, 2010
    I think I can safely say that we’re all Python evangelists.  In fact, I’m pretty sure my first conversation with ‘FixedByDrift’ revolved around just how enamored with Python he is.  Likewise my first email with ‘AmbiguousBase’ was a code exchange of microsatellite finding software written in Python. We just love Python. So why should you learn to love Python […]

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