Introduction to Perl for Bioinformatics
Description
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 complement to
traditional programming languages (C/C++) or shell scripting languages
and editors. Perl is available for most computing environments and can
be downloaded and installed free of charge.
The first day of this course will cover a broad range of the core
features of the Perl programming language, including the language
syntax, functions, library modules, regular expressions, and some
object-oriented features. The course also explores invocation options,
debugging, common mistakes, and much more.
The second day of the course will focus on using Perl programming
in Bioinformatics. Topics will include querying dna strings, reading
dna from Fasta files, parsing GenBank annotations, parsing PDB files,
parsing BLAST output, using Perl modules like bioperl, etc.
Both days will include lab time for writing Perl solutions to
exercises provided in the training notes.
Prerequisites
Some prior programming experience (particularly in C/C++)
will be helpful, but is not essential
Target Audience
Persons interested in learning the fundamentals (or
expanding their knowledge) of Perl, and how Perl might facilitate
bioinformatics investigation. Individuals interested in Perl, but not
bioinformatics, are encouraged to register and attend day one.
Method of Delivery
Lecture with hands-on exercises
Handouts
February 2005, Part One PDF,
Pete Carswell
February 2005, Part Two PDF,
Pete Carswell
November 2004, Part One PDF, Pete
Carswell
November 2004, Part Two PDF,
Pete Carswell
Tutorial #5, OCCBIO '08, June 2-4, 2008, Toledo, Ohio:
Using Perl in the Identification of CIS Elements in Promoter Sequences of Rice Genes, Presenters: Peter Carswell and Yuan Zhang, Ohio Supercomputer Center
Introduction to Perl Scripting (pdf)
Analysis of Rice DNA (pdf)
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