Abstract
Inversions are a class of chromosomal mutations, widely regarded as one of the major mechanisms for reorganizing the genome.
In this paper we present a new algorithm for the approximate string matching problem allowing for non-overlapping inversions which runs in \(\mathcal{O} (nm)\) worst-case time and \(\mathcal{O} (m^2)\)-space, for a character sequence of size n and pattern of size m. This improves upon a previous \(\mathcal{O} (nm^2)\)-time algorithm.
This work has been partly supported by G.N.C.S., Istituto Nazionale di Alta Matematica “Francesco Severi”.
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Cantone, D., Cristofaro, S., Faro, S. (2011). Efficient Matching of Biological Sequences Allowing for Non-overlapping Inversions. In: Giancarlo, R., Manzini, G. (eds) Combinatorial Pattern Matching. CPM 2011. Lecture Notes in Computer Science, vol 6661. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21458-5_31
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DOI: https://doi.org/10.1007/978-3-642-21458-5_31
Publisher Name: Springer, Berlin, Heidelberg
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