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.
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
Publisher: Oxford University Press, USA
Distributor: Oxford University Press USA
Publication Date: 08-10-2007
Pages: 288
Measurements: 7.000in X 9.800in X 0.600in X 1.094lb
