A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and k-Mer DistancesReport as inadecuate




A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and k-Mer Distances - Download this document for free, or read online. Document in PDF available to download.

1 LIFL - Laboratoire d-Informatique Fondamentale de Lille 2 BONSAI - Bioinformatics and Sequence Analysis LIFL - Laboratoire d-Informatique Fondamentale de Lille, Inria Lille - Nord Europe 3 NCSU - North Carolina State University Raleigh

Abstract : Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014, and to provide a lower misclassification rate when used with Support Vector Machines SVMs On-odera and Shibuya, 2013, We confirm by independent experiments these two results, and propose in this article to use a coverage criterion Benson and Mak, 2008, Martin, 2013, Martin and Noé, 2014, to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification-the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.

Keywords : Spaced seed Spaced k-mer Gapped k-mer Coverage sensitivity Support Vector Machine String kernel Alignment-free distance





Author: Laurent Noé - Donald E. K. Martin -

Source: https://hal.archives-ouvertes.fr/



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