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

Download all sourcecode in the book.
See below for install directions and assignments. (as of Fall 2009)

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 2009 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 (zip) (now requires docs in pod; updated Aug. 12, 2009)

Chapter 5: Time to do the math

Program #2: Chargaff's Numbers (zip) (now requires docs in pod; updated Sept. 17, 2009)

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