The out-of-place testing for genome comparison

4^th International Conference and Exhibition on Biometrics & Biostatistics

November 16-18, 2015 San Antonio, USA

Hsin-Hsiung Huang

University of Central Florida, USA

Scientific Tracks Abstracts: J Appl Computat Math

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.

Biography :

Hsin-Hsiung Huang has completed his PhD from the University of Illinois at Chicago and has been a one-year visiting Assistant Professor of the Department of Statistics at the University of Central Florida. He is now a Tenure-Track Assistant Professor of the Department of Statistics at the University of Central Florida. He has published 5 papers in reputed journals.

Email: hsin.huang@ucf.edu