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Genomics and proteomics: a signal processor's tour

Vaidyanathan, P. P. (2004) Genomics and proteomics: a signal processor's tour. IEEE Circuits and Systems Magazine, 4 (4). pp. 6-29. ISSN 1531-636X. http://resolver.caltech.edu/CaltechAUTHORS:VAIieeecsm04

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Abstract

The theory and methods of signal processing are becoming increasingly important in molecular biology. Digital filtering techniques, transform domain methods, and Markov models have played important roles in gene identification, biological sequence analysis, and alignment. This paper contains a brief review of molecular biology, followed by a review of the applications of signal processing theory. This includes the problem of gene finding using digital filtering, and the use of transform domain methods in the study of protein binding spots. The relatively new topic of noncoding genes, and the associated problem of identifying ncRNA buried in DNA sequences are also described. This includes a discussion of hidden Markov models and context free grammars. Several new directions in genomic signal processing are briefly outlined in the end.


Item Type:Article
Additional Information:© Copyright 2004 IEEE. Reprinted with permission. It is my pleasure to thank Professors A. Antoniou, L. Bruton, and M.N.S. Swamy, for strongly encouraging me to write this article. I am grateful to Professor M. Ogorzalek for all his support and help during the production of this article. Many of the Fourier transform and digital filtering plots in this paper were prepared by Mr. Byung-Jun Yoon, graduate student at the California Institute of Technology. Work supported in part by the ONR grant N00014-99-1-1002.
Subject Keywords:Genomic-signal-processing, bioinformatics, genes, protein-coding, DNA, ncRNA
Record Number:CaltechAUTHORS:VAIieeecsm04
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:VAIieeecsm04
Alternative URL:http://dx.doi.org/10.1109/MCAS.2004.1371584
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9665
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:25 Feb 2008
Last Modified:26 Dec 2012 09:51

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