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A New Combinatorial Approach to Sequence Comparison

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Abstract

In this paper we introduce a new alignment-free method for comparing sequences which is combinatorial by nature and does not use any compressor nor any information-theoretic notion. Such a method is based on an extension of the Burrows-Wheeler Transform, a transformation widely used in the context of Data Compression. The new extended transformation takes as input a multiset of sequences and produces as output a string obtained by a suitable rearrangement of the characters of all the input sequences. By using such a transformation we give a general method for comparing sequences that takes into account how much the characters coming from the different input sequences are mixed in the output string. Such a method is tested on a real data set for the whole mitochondrial genome phylogeny problem. However, the goal of this paper is to introduce a new and general methodology for automatic categorization of sequences.

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Authors and Affiliations

  1. Dipartimento di Matematica ed Appl., University of Palermo, via Archirafi 34, 90123, Palermo, Italy

    S. Mantaci, A. Restivo, G. Rosone & M. Sciortino

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  1. S. Mantaci
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  2. A. Restivo
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  3. G. Rosone
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  4. M. Sciortino
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Corresponding author

Correspondence to M. Sciortino.

Additional information

This work was partially supported by the Italian MIUR PRIN project “Automi e Linguaggi Formali: aspetti matematici ed applicativi” and by MIUR FIRB Italy-Israel project “Pattern Matching and Discovery in Discrete Structures, with applications to Bioinformatics”.

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Mantaci, S., Restivo, A., Rosone, G. et al. A New Combinatorial Approach to Sequence Comparison. Theory Comput Syst 42, 411–429 (2008). https://doi.org/10.1007/s00224-007-9078-6

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  • DOI: https://doi.org/10.1007/s00224-007-9078-6

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