An estimator for local analysis of genome based on the minimal absent word

Lianping Yang; Xiangde Zhang; Haoyue Fu; Chenhui Yang

doi:10.1016/j.jtbi.2016.01.023

An estimator for local analysis of genome based on the minimal absent word

J Theor Biol. 2016 Apr 21:395:23-30. doi: 10.1016/j.jtbi.2016.01.023. Epub 2016 Jan 29.

Authors

Lianping Yang¹, Xiangde Zhang², Haoyue Fu³, Chenhui Yang⁴

Affiliations

¹ College of Sciences, Northeastern University, Wenhua Road, 110004 Shenyang, China. Electronic address: yanglp@mail.neu.edu.cn.
² College of Sciences, Northeastern University, Wenhua Road, 110004 Shenyang, China. Electronic address: zhangxdneu@163.com.
³ College of Sciences, Northeastern University, Wenhua Road, 110004 Shenyang, China.
⁴ School of Information Science and Engineering, Xiamen University, China.

PMID: 26829314
DOI: 10.1016/j.jtbi.2016.01.023

Abstract

This study presents an alternative alignment-free relative feature analysis method based on the minimal absent word, which has potential advantages over the local alignment method in local analysis. Smooth-local-analysis-curve and similarity-distribution are constructed for a fast, efficient, and visual comparison. Moreover, when the multi-sequence-comparison is needed, the local-analysis-curves can illustrate some interesting zones.

Keywords: Alignment-free; Relative feature; Visual comparison.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Genome, Human*
Humans
Models, Genetic*
Sequence Analysis, DNA*