title: Identification of CpG islands in DNA sequences using matched filters.
abstract: CpG islands (CGIs), rich in CG dinucleotides, are usually located in the promoter regions of genes in DNA sequences and are used as gene markers. Identification of CGIs plays an important role in the analysis of DNA sequences. In this paper, we propose a new digital signal processing (DSP) based approach using matched filters for the identification of CGIs. We also formulate a new/reliable CGI identification characteristic replacing the several existing probability transition tables for CGIs and non-CGIs. The peaks in matched filter output, obtained by correlating the CGI characteristic with the DNA sequence to be analyzed, accurately and reliably identify CGIs. This approach is tested on a number of DNA sequences and is proved to be capable of identifying CpG islands efficiently and reliably.
authors.affiliation: Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd, WestMontreal, Quebec H3G1M8, Canada.
authors.forename: Rajasekhar
authors.initials: R
authors.lastname: Kakumani
authors.forename: M Omair
authors.initials: MO
authors.lastname: Ahmad
authors.forename: Vijay
authors.initials: V
authors.lastname: Devabhaktuni
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D018899:CpG Islands / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA