Parsing Blast output (Part II)

Topics

• Modifying a parser of Blast output
• Resolution of scenario
• Luke Chaney presents:
  Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project
  Tettelin H, Radune D, Kasif S, Khouri H, and Salzberg SL
  Genomics (1999) 62: 500-507.
• Luke Chaney presents:
  The Life and Times of Hoda Khouri

• Notes: (none)
• Program: Parse-Blast.tru, a program to parse Blast output. Modify this program to run on the output you generated from local Blast.
• Library: Utilities.trc, used by Parse-Blast.tru
• Data: alr2168Vs7120CMR.txt, CMR-BlastN-generated file used by current version of Parse-Blast.tru. Given so you can see the current version run.
• Notes: How to get the given program to work on its own data. You can ignore this, if you like, and just start with the working program below.
• Program: Parse-Blast-revised.tru, a revised version of Parse-Blast that actually works (on the CMR-BlastN-generated file). Modify this program to run on the output you generated from local Blast.
• Notes: How to get revised program to work on local BlastN output.
• Notes: How to get revised program to work on local TBlastX output.
• Notes: How to use Excel to analyze parsed output from BlastN
• Notes: How to use Excel to analyze parsed output from TBlastX
• Questionnaire: (none)

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