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Revision as of 14:56, 12 February 2012 by ShawnDouglas (Talk | contribs)
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  • / - given target sequence, generate oligos that can be used for PCR assembly of that sequence
  • / - generate random DNA sequence of specified length
  • / - given upstream and downstream sense sequence of region to amplify, print out correct primers


  • / - given input sequence generate N-mers orthogonal (to seq and its complement) to be used as toeholds
  • / - Tk GUI for honeycomb lattice program

DNA sequence manipulation

  • reverse complement & remove whitespace
complement = string.maketrans('ACGTacgt','TGCAtgca')
def comp(s):
  return s.translate(complement)[::-1]
def nowhite(s):
  return ''.join([c for c in s if c in string.letters])

  • replace mac return character ('\r') with unix return ('\n')
cat foo | tr '\r' '\n' > bar
mv bar foo
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