Approximate string-matching with a single gap for sequence alignment

Authors:
Tomáš Flouri;Kunsoo Park;Kimon Frousios;Solon P. Pissis;Costas S. Iliopoulos;German Tischler
Affiliations:
Czech Technical University, Prague;Seoul National University, Seoul, South Korea;King's College London, Strand, London, England, United Kingdom;King's College London, Strand, London, England, United Kingdom;King's College London, Strand, London, England, United Kingdom;University of Würzburg, Am Hubland, Würzburg, Germany
Venue:
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Year:
2011

Citing 1
Cited 1

Algorithms on strings, trees, and sequences: computer science and computational biology

Algorithms on strings, trees, and sequences: computer science and computational biology

GapsMis: flexible sequence alignment with a bounded number of gaps

Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics

Quantified Score

Hi-index	0.00

Visualization

Abstract

This paper deals with the approximate string-matching problem with Hamming distance and a single gap for sequence alignment. We consider an extension of the approximate string-matching problem with Hamming distance, by also allowing the existence of a single gap, either in the text, or in the pattern. This problem is strongly and directly motivated by the next-generation re-sequencing procedure. We present a general algorithm that requires O (nm) time, where n is the length of the text and m is the length of the pattern, but this can be reduced to O (mβ) time, if the maximum length β of the gap is given.