NDLI: Optimized numerical mapping scheme for filter-based exon location in DNA using a quasi-Newton algorithm

Content Provider	IEEE Xplore Digital Library
Author	Ramachandran, P. Wu-Sheng Lu Antoniou, A.
Copyright Year	2010
Description	Author affiliation: Department of Electrical and Computer Engineering University of Victoria, BC, Canada, V8W 3P6 (Ramachandran, P.; Wu-Sheng Lu; Antoniou, A.)
Abstract	An optimized numerical mapping scheme for achieving improved location of exons in DNA sequences using digital filters is proposed. Characteristic numerical values for the four nucleotides, referred to as pseudo-EIIP values, are obtained using a training procedure where the location accuracy is maximized using a quasi-Newton algorithm based on the Broyden-Fletcher-Goldfarb-Shanno updating formula. A training set of 80 DNA sequences is chosen from the HMR195 database. The objective function for the optimization procedure is formulated using the so-called receiver operating characteristic (ROC) technique and the procedure is initialized using electron-ion interaction potential (EIIP) values. Unbiased testing of the optimized characteristic values is carried out using a set of DNA sequences that has no overlap with the training set. Simulation results show that the pseudo-EIIP values yield more accurate exon locations than those obtained using the actual EIIP values.
Starting Page	2231
Ending Page	2234
File Size	249625
Page Count	4
File Format	PDF
ISBN	9781424453085
DOI	10.1109/ISCAS.2010.5537209
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-05-30
Publisher Place	France
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	DNA Sequences Digital filters Frequency Computational efficiency Charge carrier processes Testing Databases Organisms Proteins ROC plots exons period-3 property electron-ion interaction potential bandpass notch digital filters BFGS updating formula
Content Type	Text
Resource Type	Article

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