Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology

ISBN-13: 9780521585194 / Angielski / Twarda / 1997 / 556 str.

Dan Gusfield

Opis

Traditionally an area of study in computer science, string algorithms have, in recent years, become an increasingly important part of biology, particularly genetics. This volume is a comprehensive look at computer algorithms for string processing. In addition to pure computer science, Gusfield adds extensive discussions on biological problems that are cast as string problems and on methods developed to solve them. This text emphasizes 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, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics.

Recenzje

'… could well be used as the basis for a graduate-level course, particularly as it contains over 400 exercises to reinforce presented material and to develop further topics. It is recommended most highly.' P. Gibbons, Zentralblatt für Mathematik

Spis treści

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.