Biometrics & Biostatistics

Biography

Biography: Hsin-Hsiung Huang

Abstract

The out-of-place distance measure with alignment-free n-gram based method has been successfully applied to automatic text or natural languages categorization in real time. Like k-mers, n-grams are sub-sequences of length ‘n’ from a given sequence, but the ways of computing the number of n-grams and k-mers are different. Additionally, it is not clear about its performance and the selection of ‘n’ for comparing genome sequences. In this study, the author proposed a symmetric version of the out-of-place measure, a non-parametric out-of-place measure, and an approach for finding the optimal range of ‘n’ to construct a phylogenetic tree with the symmetric out-of-place measures. This approach, then, is applied to four mitochondrial genome sequence data-sets. The resulting phylogenetic trees are similar to the standard biological classification. It shows that the proposed method is a very powerful tool for phylogenetic analysis in terms of both classification accuracy and computation efficiency.