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

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 book is a general te...

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Bibliographic Details
Main Author: Dan Gusfield
Format: Printed Book
Published: Cambridge University Press 2005
Subjects:
Computer algorithms. Computational biology. Molecular biology > Data processing.
Table of Contents:
  • Exact matching: fundamental preprocessing and first algorithms
  • Exact matching: classical comparison-based methods
  • Exact matching: a deeper look at classical methods
  • Seminumerical string matching
  • Introduction to suffix trees
  • Linear-time construction of suffix trees
  • First applications of suffix trees
  • Constant-time lowest common ancestor retrieval
  • More applications of suffix trees
  • The importance of (sub)sequence comparison in molecular biology
  • Core string edits, alignments, and dynamic programming
  • Refining core string edits and alignments
  • Extending the core problems
  • Multiple string comparison
  • The Holy Grail
  • sequence databases and their uses- The Mother Lode
  • Maps, mapping, sequencing, and superstrings
  • Strings and evolutionary trees
  • Three short topics
  • Models of Genome-level mutations.

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