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Identification of CpG islands using a bank of IIR lowpass filters

Yoon, Byung-Jun and Vaidyanathan, P. P. (2004) Identification of CpG islands using a bank of IIR lowpass filters. In: IEEE Digital Signal Processing Workshop,11th, and the 3rd IEEE Signal Processing Education Workshop, Taos Ski Valley, NM, 1-4 August 2004. IEEE , Piscataway, NJ, pp. 315-319. ISBN 0780384342 http://resolver.caltech.edu/CaltechAUTHORS:YOOdwpws04

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Abstract

It has been known that biological sequences such as the DNA sequence display different kinds of patterns depending on their biological functions. This statistical difference can be exploited for identifying the region of interest, such as the protein coding regions or CpG islands, in a new biological sequence that has not been annotated yet. A region of particular interest is the CpG island, which is a region in a DNA sequence that is rich in the dinucleotide CpG, since it is known that they can be used as gene markers. There have been several computational methods for identifying CpG islands, each with its own strength and weakness. In this paper, we propose a novel scheme for detecting CpG islands in a genomic sequence, which is based on a bank of IIR lowpass filters. The proposed method is capable of identifying CpG islands efficiently at a low computational expense. Simulation results are included where appropriate to demonstrate the idea.


Item Type:Book Section
Additional Information:© 2004 IEEE. Reprinted with Permission. Publication Date: 1-4 Aug. 2004. Posted online: 2005-06-13. Work supported in part by the ONR grant N00014-99-1-1002, USA.
Subject Keywords:DNA; IIR filters; genetics; low-pass filters; medical signal processing; molecular biophysics; proteins; sequences; CpG dinucleotide; CpG island identification; DNA sequence detection; IIR lowpass filter bank; biological sequence patterns; digital signal processing; gene markers; genomic sequence; protein coding regions
Record Number:CaltechAUTHORS:YOOdwpws04
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:YOOdwpws04
Alternative URL:http://dx.doi.org/10.1109/DSPWS.2004.1437966
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9707
Collection:CaltechAUTHORS
Deposited By: Kristin Buxton
Deposited On:05 Mar 2008
Last Modified:26 Dec 2012 09:51

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