Identification of CpG islands in DNA sequences using matched filters

Rajasekhar Kakumani; M Omair Ahmad; Vijay Devabhaktuni

doi:10.1109/IEMBS.2011.6091490

Identification of CpG islands in DNA sequences using matched filters

Annu Int Conf IEEE Eng Med Biol Soc. 2011:2011:6029-32. doi: 10.1109/IEMBS.2011.6091490.

Authors

Rajasekhar Kakumani¹, M Omair Ahmad, Vijay Devabhaktuni

Affiliation

¹ Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd, WestMontreal, Quebec H3G1M8, Canada.

PMID: 22255714
DOI: 10.1109/IEMBS.2011.6091490

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.

Publication types

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

MeSH terms

Algorithms*
Base Sequence
CpG Islands / genetics*
DNA / genetics*
Molecular Sequence Data
Sequence Analysis, DNA / methods*

Substances

DNA