1. Modification of the bioperl script for parsing BLAST output

2. 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)

3. Criteria
E value
Fraction (the fraction of query sequences being aligned)
Similarity

4. E value Position # E VALUE CRITERION GOES HERE!!! code
next if ($e > );

5. Fraction Position # FRACTION CRITERION GOES HERE!!! code
my $frac = ($qend - $qstart) / $qlength;
next if ($frac < 0.95);

6. Similarity Position # SIMILARITY CRITERION GOES HERE!!! code
next if ($conserved < 95);