eprintid: 8356
rev_number: 2
eprint_status: archive
userid: 1
dir: disk0/00/00/83/56
datestamp: 2023-11-09 16:20:15
lastmod: 2023-11-09 16:20:15
status_changed: 2023-11-09 16:12:27
type: article
metadata_visibility: show
creators_name: Ahmad, M.
creators_name: Jung, L.T.
creators_name: Bhuiyan, A.-A.
title: A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing
ispublished: pub
keywords: Adaptive filters; Bandpass filters; Bioinformatics; Codes (symbols); Digital signal processing; DNA; Fuzzy filters; Gene encoding; Median filters; Nucleotides; Signal noise measurement, 1/F noise; 3-base periodicity; Conventional filters; Digital signal processing techniques; Fundamental characteristics; Fuzzy adaptive filters; Strong correlation; Window filters, Signal processing, DNA; nucleotide; DNA, 3 base periodicity; accuracy; algorithm; Article; codon; DNA sequence; DNA strand; DNA structure; fuzzy adaptive window median filter; fuzzy system; genetic code; human; molecular biology; nonhuman; nucleotide sequence; signal noise ratio; signal processing; algorithm; biology; chemistry; fuzzy logic; procedures, Algorithms; Computational Biology; DNA; Fuzzy Logic; Signal Processing, Computer-Assisted
note: cited By 13
abstract: Background and Objective Digital signal processing techniques commonly employ fixed length window filters to process the signal contents. DNA signals differ in characteristics from common digital signals since they carry nucleotides as contents. The nucleotides own genetic code context and fuzzy behaviors due to their special structure and order in DNA strand. Employing conventional fixed length window filters for DNA signal processing produce spectral leakage and hence results in signal noise. A biological context aware adaptive window filter is required to process the DNA signals. Methods This paper introduces a biological inspired fuzzy adaptive window median filter (FAWMF) which computes the fuzzy membership strength of nucleotides in each slide of window and filters nucleotides based on median filtering with a combination of s-shaped and z-shaped filters. Since coding regions cause 3-base periodicity by an unbalanced nucleotides' distribution producing a relatively high bias for nucleotides' usage, such fundamental characteristic of nucleotides has been exploited in FAWMF to suppress the signal noise. Results Along with adaptive response of FAWMF, a strong correlation between median nucleotides and the Πshaped filter was observed which produced enhanced discrimination between coding and non-coding regions contrary to fixed length conventional window filters. The proposed FAWMF attains a significant enhancement in coding regions identification i.e. 40 to 125 as compared to other conventional window filters tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. Conclusion This study proves that conventional fixed length window filters applied to DNA signals do not achieve significant results since the nucleotides carry genetic code context. The proposed FAWMF algorithm is adaptive and outperforms significantly to process DNA signal contents. The algorithm applied to variety of DNA datasets produced noteworthy discrimination between coding and non-coding regions contrary to fixed window length conventional filters. © 2017 Elsevier B.V.
date: 2017
publisher: Elsevier Ireland Ltd
official_url: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85024392052&doi=10.1016%2fj.cmpb.2017.06.021&partnerID=40&md5=53f541d8d9b7fef9068114a39891b779
id_number: 10.1016/j.cmpb.2017.06.021
full_text_status: none
publication: Computer Methods and Programs in Biomedicine
volume: 149
pagerange: 11-17
refereed: TRUE
issn: 01692607
citation:   Ahmad, M. and Jung, L.T. and Bhuiyan, A.-A.  (2017) A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing.  Computer Methods and Programs in Biomedicine, 149.  pp. 11-17.  ISSN 01692607