Traditionally an area of study in computer science, string algorithms have, in recent years, become an increasingly important part of biology, particularly genetics.
Dan Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, Cambridge University Press; 1 edition (May 28, 1997):
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.
W.F. Smyth, Compputing Patterns in Strings, Pearson Addison Wesley (Uk), 2003:
The computation of patterns in strings is a fundamental requirement in many areas of science and information processing. The operation of a text editor, the lexical analysis of a computer program, the functioning of a finite automaton, the retrieval of information from a database - these are all activities which may require that patterns be located and computed. In other areas of science, the algorithms that compute patterns have applications in such diverse fields as data compression, cryptography, speech recognition, computer vision, computational geometry and molecular biology.
Flexible Pattern Matching in Strings: Practical On-Line Search Algorithms for Texts and Biological Sequences:
Recent years have witnessed a dramatic increase of interest in sophisticated string matching problems, especially in information retrieval and computational biology. This book presents a practical approach to string matching problems, focusing on the algorithms and implementations that perform best in practice. It covers searching for simple, multiple and extended strings, as well as regular expressions, and exact and approximate searching. It includes all the most significant new developments in complex pattern searching. The clear explanations, step-by-step examples, algorithm pseudocode, and implementation efficiency maps will enable researchers, professionals and students in bioinformatics, computer science, and software engineering to choose the most appropriate algorithms for their applications.
