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 image (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

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