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BMCBI
2010

MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences

13 years 2 months ago
MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences
Background: While multiple alignment is the first step of usual classification schemes for biological sequences, alignment-free methods are being increasingly used as alternatives when multiple alignments fail. Subword-based combinatorial methods are popular for their low algorithmic complexity (suffix trees ...) or exhaustivity (motif search), in general with fixed length word and/or number of mismatches. We developed previously a method to detect local similarities (the N-local decoding) based on the occurrences of repeated subwords of fixed length, which does not impose a fixed number of mismatches. The resulting similarities are, for some "good" values of N, sufficiently relevant to form the basis of a reliable alignment-free classification. The aim of this paper is to develop a method that uses the similarities detected by N-local decoding while not imposing a fixed value of N. We present a procedure that selects for every position in the sequences an adaptive value of ...
Eduardo Corel, Florian Pitschi, Ivan Laprevotte, G
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Eduardo Corel, Florian Pitschi, Ivan Laprevotte, Gilles Grasseau, Gilles Didier, Claudine Devauchelle
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