Main description:

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.

Contents:

1. Introduction: Explorations and Indexes ; 2. Essential First Steps ; 3. Playing with DNA Sequences (and words) Using Regular Expressions ; 4. Your First Perl Programs with a Focus on String Analysis ; 5. Using Perl to Do Calculations ; 6. Making Decisions Over and Over Again with Perl's "if" and "while" ; 7. Subroutines ; 8. Accessing Files of Sequences from Databases ; 9. Arrays ; 10. Hash Tables ; 11. Phrasing Questions by Writing Algorithms ; 12. Regular Expressions Revisited ; 13. Understanding Randomness ; 14. Modules ; 15. Conclusions ; Appendix I ; Appendix II ; Bibliography