Mathematical Concepts and Methods in Modern Biology

Chapter 9

Identifying CpG Islands: Sliding Window and Hidden Markov Model Approaches

Raina Robeva^*, Aaron Garrett^†, James Kirkwood^* and Robin Davies^‡, ^*Department of Mathematical Sciences, Sweet Briar College, Sweet Briar, VA, USA, ^†Department of Mathematical, Computing, and Information Sciences, Jacksonville State University, Jacksonville, AL, USA, ^‡Department of Biology, Sweet Briar College, Sweet Briar, VA, USA

9.1 Introduction

The dinucleotide (a cytosine followed by a guanine on a single DNA strand) has a pattern of non-homogeneity along the genome. Regions of relatively low frequencies are interrupted by clusters with markedly higher