Perl for Exploring DNA
by
Mark D. LeBlanc and Betsey D. Dyer
Oxford University Press
(July 2007)

Download all sourcecode in the book.

Installing perl and a programming environment

for Mac OS X

Download PDF Instructions

for Windows® 2000/XP

Download PDF instructions

Syllabus

BIO/COMP 242 - "DNA"

Download Fall 2007 Syllabus (pdf)

Sample Programming Assignments

Chapter 4: Regex Play

Program #0: Regex Play (zip)

More Play with Regex (zip)

Chapter 3: Playing with Strings (Your First Perl Program)

Program #1: String Play (pdf)

Chapter 5: Time to do the math

Program #2: Chargaff's Numbers (zip)

Chapter 6: Control Structures (conditionals)

Program #3: mini Gene Finder (zip)

Chapter 6: Control Structures (loops and regex)

Program #4: Upstream Repeat Finder (zip)

Chapter 7: Subroutines (modular code and more regex)

Program #5 setup: BLASTing seven transmembrane proteins (pdf)

Program #5: Fuzzy Olfaction Gene Finder (zip)

Chapter 9: Arrays and Hashes (Comparative Genomics)

Program #6: Comparative Genomics: finding the most-frequently occurring motifs (.zip)

FInal Projects

Project Suggestions, Timeline, Intro-Methods Grade Key, Oral Presentation Grade Key