Modification of the bioperl script for parsing BLAST output

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)

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

E value Position # E VALUE CRITERION GOES HERE!!! code next if ($e > 0.00001);

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

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