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 define a measure to compare sequences that takes into account how the characters coming from 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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Mantaci, S., Restivo, A., Rosone, G., Sciortino, M. (2005). A New Combinatorial Approach to Sequence Comparison. In: Coppo, M., Lodi, E., Pinna, G.M. (eds) Theoretical Computer Science. ICTCS 2005. Lecture Notes in Computer Science, vol 3701. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11560586_28
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DOI: https://doi.org/10.1007/11560586_28
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