Academic Journal
A New Combinatorial Approach to Sequence Comparison.
| Title: | A New Combinatorial Approach to Sequence Comparison. |
|---|---|
| Authors: | Mantaci, S.1 sabrina@math.unipa.it, Restivo, A.1 restivo@math.unipa.it, Rosone, G.1 giovyros@virgilio.it, Sciortino, M.1 mari@math.unipa.it |
| Source: | Theory of Computing Systems. Apr2008, Vol. 42 Issue 3, p411-429. 19p. 1 Diagram, 6 Charts. |
| Subject Terms: | *Programmable controllers, *Database management, Combinatorics, Programmable sequence controllers, Coding theory, Data compression |
| 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. [ABSTRACT FROM AUTHOR] |
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| Database: | Business Source Index |
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