16,039 research outputs found
A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances
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 No{\'e}, 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.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017
A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances
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 No{\'e}, 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.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017
Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics
Next Generation Sequencing (NGS) technologies generate large amounts of short
read data for many different organisms. The fact that NGS reads are generally
short makes it challenging to assemble the reads and reconstruct the original
genome sequence. For clustering genomes using such NGS data, word-count based
alignment-free sequence comparison is a promising approach, but for this
approach, the underlying expected word counts are essential.
A plausible model for this underlying distribution of word counts is given
through modelling the DNA sequence as a Markov chain (MC). For single long
sequences, efficient statistics are available to estimate the order of MCs and
the transition probability matrix for the sequences. As NGS data do not provide
a single long sequence, inference methods on Markovian properties of sequences
based on single long sequences cannot be directly used for NGS short read data.
Here we derive a normal approximation for such word counts. We also show that
the traditional Chi-square statistic has an approximate gamma distribution,
using the Lander-Waterman model for physical mapping. We propose several
methods to estimate the order of the MC based on NGS reads and evaluate them
using simulations. We illustrate the applications of our results by clustering
genomic sequences of several vertebrate and tree species based on NGS reads
using alignment-free sequence dissimilarity measures. We find that the
estimated order of the MC has a considerable effect on the clustering results,
and that the clustering results that use a MC of the estimated order give a
plausible clustering of the species.Comment: accepted by RECOMB-SEQ 201
Symmetry and Minimum Principle at the Basis of the Genetic Code
The importance of the notion of symmetry in physics is well established:
could it also be the case for the genetic code? In this spirit, a model for the
Genetic Code based on continuous symmetries and entitled the "Crystal Basis
Model" has been proposed a few years ago. The present paper is a review of the
model, of some of its first applications as well as of its recent developments.
Indeed, after a motivated presentation of our mathematical model, we illustrate
its pertinence by applying it for the elaboration and verification of sum rules
for codon usage probabilities, as well as for establishing relations and some
predictions between physical-chemical properties of amino-acids. Then, defining
in this context a "bio-spin" structure for the nucleotides and codons, the
interaction between a couple of codon-anticodon can simply be represented by a
(bio) spin-spin potential. This approach will constitute the second part of the
paper where, imposing the minimum energy principle, an analysis of the
evolution of the genetic code can be performed with good agreement with the
generally accepted scheme. A more precise study of this interaction model
provides informations on codon bias, consistent with data.Comment: To appear in BIOMAT 2016, 326 - 362, 201
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