Optimal spaced seeds for faster approximate string matching

Authors:
Martin Farach-Colton;Gad M. Landau;S. Cenk Sahinalp;Dekel Tsur
Affiliations:
Department of Computer Science and DIMACS, Rutgers University, USA;Department of Computer Science, University of Haifa, Israel;Laboratory for Computational Biology, Simon Fraser University, Canada;Department of Computer Science, Ben-Gurion University of the Negev, Israel
Venue:
Journal of Computer and System Sciences
Year:
2007

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Abstract

Optimal spaced seeds were introduced by the theoretical computer science community to bioinformatics to effectively increase homology search sensitivity. These seeds are serving many homology queries daily. However the computational complexity of finding ...