Links & References

Web Resources


Gonzalo Navarro, Mathieu Raffinot
Flexble Pattern matching in Strings: Practical On-Line Search Algorithms for Texts and Biological Sequences, Cambridge University Press, 2002
[ Navarro -- book homepage ] [ Google Books ] [ ACM portal ]

Maxime Crochemore, Wojciech Rytter
Jewels of Stringology: Text Algorithms, World Scientific Publishing, 2003

[ Amazon ]

Dan Gusfield
Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology., Cambridge University Press, 1997

A. Aho
Algorithms for finding patterns in strings. In Handbook of Theoretical Computer Science, Vol. A, pp255-300. Elsevier, 1990

Cormen, T.H., Leiserson, C.E., Rivest, R.L.
Introduction to Algorithms, Chapter 34 (String Matching), MIT Press, 1990

  1. Ricardo Baeza-Yates, Berthier Ribeiro-Neto: Modern Information Retrieval, Addison Wesley
  2. Durbin, R., Eddy, S., Krogh, A., Mitchison - Biological sequence analysis - Probabilistic models of proteins and nucleic acids (Cambridge University Press, 1998)
  3. Jorma Tarhio, Merkkijonomenetelmät (luentomoniste) ~ 1995 University of Helsinki
  4. Pevzner, P.A. Computational Molecular Biology - An Algorithmic Approach (MIT Press, 2000)
  5. Baldi, Pierre, and Brunak, Soren, Bioinformatics - the Machine Learning Approach 2nd edition, (MIT Press, 2001)


Commentz-Walter: You can download here my algorithm StringMatchingFastOnTheAverage (PDF, ~17,2 MB) or here StringMatchingFastOnTheAverage (extended abstract) (PDF, ~3 MB)

Video lectures

Graph edit distance

Pattern analysis:

Mehryar Mohri, Weighted Transducers and Rational Kernels

Similarity and differences by finite automata Tamás Gaál, XEROX Research Centre Europe

Ewan Birney and many other bioinformatics folks on open publishing:

Trivia: Face recognition - people in computer science, bioinformatics, bio