Tutorial VIII: Perl Tools for Bioinformatics

Pete Carswell, Systems Developer/Engineer, Ohio Supercomputer Center
Location: Shriver Center
Monday 1:30 p.m. - 3:00 p.m.

Perl is a general-purpose interpreted language that is optimized for text and file manipulation, I/O, and system tasks. It provides a simple and efficient way to do many jobs and acts as a compliment to traditional programming languages (C/C++), shell scripting languages and editors or internet CGI. Perl is available for most computing environments and can be downloaded and installed free of charge.

Perl is an ideal scripting language for processing files, looking for a particular pattern of characters, or for reformatting data tables. This powerful regular expression capability for pattern matching and integral file manipulation are invaluable for bioinformatics, where it is common to look for motifs within sequences or rearrange one database format into another.

During this talk we will look at selected bioinformatics problems and their solutions using Perl scripts. These applications would include such popular bioinformatics tools as PDB, FASTA and BLAST. Additionally, we will briefly discuss BioPerl, a collection of Perl classes, or code, used to analyze objects representing biological entities.

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