Identification of CpG islands in DNA sequences using statistically optimal null filters

In the recent years, computational methods for processing and interpreting vast amount of genomic data, generated from genome sequencing, have gained a lot of scientific interest. Genomic sequences such as deoxyribonucleic acid (DNA) consist of biological instructions which are crucial for the development and normal functioning of almost all living organisms [1]. A DNA molecule has a complex double helix structure that involves two strands, consisting of alternating sugar and phosphate groups. Attached to these sugar groups of each DNA strand are one of the four chemical bases, namely, adenine (A), thymine (T), guanine (G), and cytosine (C). A unit comprising of base, sugar, and phosphate is referred to as a nucleotide. Hydrogen bonds between the nucleotides A and T (similarly between nucleotides G and C) from the opposite strands not only stabilize the DNA molecule, but also make the two strands complimentary. Nucleotides in a DNA strand exhibit short, recurring patterns (also called sequence motifs) that are presumed to have a biological function. Identification of these patterns helps in understanding the biological information hidden in a DNA sequence. A human DNA consists of about 3 billion nucleotides and completion of genome sequencing of numerous model organisms has further proliferated genomic databases. To completely decipher, the biological information in a DNA sequence is a daunting task and development of fast, efficient, and cost effective computational techniques for the same is a big challenge.A sequence pattern that plays a crucial role in the analysis of genomes is CpG Island (CGI). A typical CGI consists high-frequency of CpG dinucleoetides, where ‘p’ refers to the phosphodiester bond between the adjacent nucleotides [1,2]. This bond is different from the hydrogen bond that exists between C and G across two strands in a DNA double helix. The length of a CGI varies from a few hundred to a few thousand base pairs (bp), but rarely exceeds 5000 bp. It