Chapter 12. BLAST

In biological research, the search for sequence similarity is very important. For instance, a researcher who has discovered a potentially important DNA or protein sequence wants to know if it's already been identified and characterized by another researcher. If it hasn't, the researcher wants to know if it resembles any known sequence from any organism. This information can provide vital clues as to the role of the sequence in the organism.

The Basic Local Alignment Search Tool (BLAST) is one of the most popular software tools in biological research. It tests a query sequence against a library of known sequences in order to find similarity. BLAST is actually a collection of programs with versions for query-to-database pairs such as nucleotide-nucleotide, protein-nucleotide, protein-protein, nucleotide-protein, and more.

This chapter examines the output from the nucleotide-nucleotide version of the program, BLASTN . For simplicity's sake, I'll simply refer to it here as BLAST. The main goal of this chapter is to show how to write code to parse a BLAST output file using regular expressions. The code is simple and basic, but it does the job. Once you understand the basics, you can build more features into your parser or obtain one of the fancier BLAST output parsers that's available via the Web. In either case, you'll know enough about output parsers to use or extend them.

This chapter also gives you a brief introduction to Bioperl, which is a collection of Perl bioinformatics modules. The Bioperl project is an example of an open source project that you, the Perl bioinformatics programmer, can put to good use. The Perl programming language is itself an open source project. The program and its source code are available for use and modification with only very reasonable restrictions and at no cost.