1 / 6

Modification of the bioperl script for parsing BLAST output

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?

loan
Download Presentation

Modification of the bioperl script for parsing BLAST output

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Modification of the bioperl scriptfor 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 > 0.00001);

  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);

More Related