NDLI: Signal Processing in Sequence Analysis: Advances in Eukaryotic Gene Prediction

Content Provider	IEEE Xplore Digital Library
Author	Akhtar, M. Epps, J. Ambikairajah, E.
Copyright Year	2007
Abstract	Genomic sequence processing has been an active area of research for the past two decades and has increasingly attracted the attention of digital signal processing researchers in recent years. A challenging open problem in deoxyribonucleic acid (DNA) sequence analysis is maximizing the prediction accuracy of eukaryotic gene locations and thereby protein coding regions. In this paper, DNA symbolic-to-numeric representations are presented and compared with existing techniques in terms of relative accuracy for the gene and exon prediction problem. Novel signal processing-based gene and exon prediction methods are then evaluated together with existing approaches at a nucleotide level using the Burset/Guigo1996, HMR195, and GENSCAN standard genomic datasets. A new technique for the recognition of acceptor splice sites is then proposed, which combines signal processing-based gene and exon prediction methods with an existing data-driven statistical method. By comparison with the acceptor splice site detection method used in the gene-finding program GENSCAN, the proposed DSP-statistical hybrid technique reveals a consistent reduction in false positives at different levels of sensitivity, averaging a 43% reduction when evaluated on the GENSCAN test set.
Sponsorship	IEEE Signal Processing Society
Starting Page	310
Ending Page	321
Page Count	12
File Size	723327
File Format	PDF
ISSN	19324553
Volume Number	2
Issue Number	3
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-06-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Signal processing Signal analysis Sequences Genomics Bioinformatics DNA Prediction methods Digital signal processing Accuracy Proteins Gaussian mixture models Autoregressive processes correlation deoxyribonucleic acid (DNA) discrete cosine transforms (DCTs) discrete Fourier transforms (DFTs)
Content Type	Text
Resource Type	Article
Subject	Signal Processing Electrical and Electronic Engineering

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