Parsing Blast output
Time: Wednesday, June 23, 9:00 am - noon
Place: Bioinformatics Computer Core Lab (Rm 104), Life Sciences Bldg
Organizer: Jeff Elhai
Audience: Primarily 1st year students

Outline of session

• Implementation of Blast on a local computer
• Parsing the output from Blast
• Pattern matching in Perl

Resources of session

• Notes: Using Blast to compare sets of protein: Parsing massive output
• Data: Proteins predicted from May 2003 assembly of Cryptospiridium (FastA format)
• Data: Proteins predicted from October 2003 assembly of Cryptospiridium (FastA format)
• Guide: How to download Blast to your own computer
• Guide: How to set up a local Blast database
• Guide: How to Blast sequences against a genome
• Program: BlastParser.pl, a program to parse Blast output
• Data: 71vsnps.txt, a test file that comes with BlastParser.
• Notes: Pattern matching in Perl

Before coming to the session

• Please look through the Scenario again if you've forgotten where we're going
• Please read the notes given above.
• Please download Blast and the two sets of proteins
• Please install a database based on one of the two sets, and compare the other set against the database
• Please take a look at BlastParser.pl
• If you run out of things to do, you can read the notes on Pattern Matching and do the exercises within, but that could be too much
• Please complete the short questionnaire (earlier the better but at least two hours before the session)

Back to Research Simulation Main Page