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

ABSTRACT:

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

SUBMITTER: Corel E 

PROVIDER: S-EPMC2923138 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature