Perl for Exploring DNA

by Mark D. LeBlanc, Betsey Dexter Dyer

Overview

This book presents Perl programming with a uniquely interdisciplinary perspective for the bioinformatics classroom. The co-authors are a professor of computer science and a professor of biology who collaborate in developing software for DNA sequence analysis. A specialty of the authors is encouraging interdisciplinary undergraduate research. The book has been tested in the classroom as a text for both biology and computer science majors. Benefiting from years of teaching experience in both computer science and biology, the authors use an exceptionally friendly and pedagogically sound introduction to Perl that emphasizes good programming practices throughout. Concepts include a rich introduction to working with strings and files of sequence data, control structures, subroutines, and data structures (e.g., arrays and hash tables). A particularly unique feature of the text is the early and repeated exposure to and use of regular expressions in sequence analysis. All examples in the book are applied to biological sequence analysis (DNA analysis, Protein analysis). The full-length book is appropriate for majors in either computer science or biology and especially relevant for new interdisciplinary courses involving students from multiple disciplines.

Product Details

ISBN-13:	9780195327571
Publisher:	Oxford University Press
Publication date:	08/10/2007
Pages:	288
Product dimensions:	10.00(w) x 7.20(h) x 0.80(d)

Table of Contents

1. Introduction: Explorations and Indexes2. Essential First Steps3. Playing with DNA Sequences (and words) Using Regular Expressions4. Your First Perl Programs with a Focus on String Analysis5. Using Perl to Do Calculations6. Making Decisions Over and Over Again with Perl's "if" and "while"7. Subroutines8. Accessing Files of Sequences from Databases9. Arrays10. Hash Tables11. Phrasing Questions by Writing Algorithms12. Regular Expressions Revisited13. Understanding Randomness14. Modules15. ConclusionsAppendix IAppendix IIBibliography