Algorithms on Strings, Trees and Sequences

String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This 1997 book is a general text on computer algorithms for string processing. In addition to pure computer science, Algorithms on Strings, Trees and Sequences contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, Algorithms on Strings, Trees and Sequences is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.

Part I. Exact String Matching: The Fundamental String Problem:
1. Exact matching: fundamental preprocessing and first algorithms
2. Exact matching: classical comparison-based methods
3. Exact matching: a deeper look at classical methods
4. Semi-numerical string matching

Part II. Suffix Trees and their Uses:
5. Introduction to suffix trees
6. Linear time construction of suffix trees
7. First applications of suffix trees
8. Constant time lowest common ancestor retrieval
9. More applications of suffix trees

Part III. Inexact Matching, Sequence Alignment and Dynamic Programming:
10. The importance of (sub)sequence comparison in molecular biology
11. Core string edits, alignments and dynamic programming
12. Refining core string edits and alignments
13. Extending the core problems
14. Multiple string comparison: the Holy Grail
15. Sequence database and their uses: the motherlode

Part IV. Currents, Cousins and Cameos:
16. Maps, mapping, sequencing and superstrings
17. Strings and evolutionary trees
18. Three short topics
19. Models of genome-level mutations