Table of Contents

Part 1: Background Basics
1. The Nucleic Acid World
2. Protein Structure
3. Dealing with Databases

Part 2: Sequence Alignments 4. Producing and Analyzing Sequence Alignments
5. Pairwise Sequence Alignment and Database Searching
6. Patterns, Profiles, and Multiple Alignments

Part 3: Evolutionary Processes 7. Recovering Evolutionary History
8. Building Phylogenetic Trees

Part 4: Genome Characteristics 9. Revealing Genome Features
10. Gene Detection and Genome Annotation

Part 5: Secondary Structures 11. Obtaining Secondary Structure from Sequence
12. Predicting Secondary Structures

Part 6: Tertiary Structures 13. Modeling Protein Structure
14. Analyzing Structure-Function Relationships

Part 7: Cells and Organisms 15. Proteome and Gene Expression Analysis
16. Clustering Methods and Statistics
17. Systems Biology

Appendices: Background Theory
Appendix A. Probability, Information, and Bayesian Analysis
Appendix B. Molecular Energy Functions
Appendix C. Function Optimization

About the Author

Marketa Zvelebil is the team leader of cancer informatics at The Breakthrough Toby Robins Breast Cancer Research Centre. Jeremy O. Baum is an Honorary Teaching Fellow in the School of Crystallography, Birkbeck College.

Reviews

'Congratulations on a fine book! I do not think I have seen such a comprehensive text on bioinformatics algorithms and techniques before. I think this will be an invaluable resource for the bioinformatics community and researchers of neighbouring disciplines.' - Jaap Heringa, Free University, Amsterdam 'This is very well done. Compared to other competing textbooks, your book will be probably the first one that explains gene finding in detail.' - Sun Kim, Indiana University, Bloomington, USA '!provides an outstanding introduction to the main bioinformatics problems and tools, well-balanced between applications to biological problems and theory behind data processing methods! an excellent and updated book for students of Bioinformatics' Computer Methods and Programs in Biomedicine