Implementating a PSSM program

Topics

• Arrays
• Common irritations and quick fixes
• Improving the program

• Notes and Study Questions
• Program: PSSM.TRU
• Program: PSortN.TRC (utility program for PSSM.TRU)
• Data: 24bp_repeat_in_Nostoc.txt (motif file for PSSM.TRU)
  List of sequences in genome of Nostoc PCC 7120 that have 4 or fewer differences relative to original 24-bp sequence.
• Data: NostocChromosome.nt (genome file for PSSM.TRU)
  Chromosome of Nostoc PCC 7120.
• Problem Set (responses to three questions due Wednesday, June 18)
  • Programs: Short programs related to problem set
  • E. coli genome (for Problem D2)
  • Response regulator motif (for Problem D4)
  • All Nostoc protein (for Problem D4)
  • cAMP-related protein (for Problem E1)
• Questionnaire

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