Modification of the bioperl script for parsing BLAST output

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Modification of the bioperl scriptfor parsing
BLAST output
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Preparation

• Download the perl script (new version) from the
  class web site
• Only one top hit and top HSP are extracted. Why?
• Flow of the code has been changed. Why?
• Open the script with perl express or notepad
  (Windows users) or Text Wrangler (Mac users)

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Criteria

• E value
• Fraction (the fraction of query sequences being
  aligned)
• Similarity

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E value

• Position
• E VALUE CRITERION GOES HERE!!!
• code
• next if (e gt 0.00001)

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Fraction

• Position
• FRACTION CRITERION GOES HERE!!!
• code
• my frac (qend - qstart) / qlength
• next if (frac lt 0.95)

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Similarity

• Position
• SIMILARITY CRITERION GOES HERE!!!
• code
• next if (conserved lt 95)