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A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing

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 beh...

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Main Authors: Ahmad, M., Jung, L.T., Bhuiyan, A.-A.
Format: Article
Published: Elsevier Ireland Ltd 2017
Online Access:https://www.scopus.com/inward/record.uri?eid=2-s2.0-85024392052&doi=10.1016%2fj.cmpb.2017.06.021&partnerID=40&md5=53f541d8d9b7fef9068114a39891b779
http://eprints.utp.edu.my/19327/
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spelling my.utp.eprints.193272018-05-03T02:12:14Z A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing Ahmad, M. Jung, L.T. Bhuiyan, A.-A. 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 Π shaped 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. Elsevier Ireland Ltd 2017 Article PeerReviewed https://www.scopus.com/inward/record.uri?eid=2-s2.0-85024392052&doi=10.1016%2fj.cmpb.2017.06.021&partnerID=40&md5=53f541d8d9b7fef9068114a39891b779 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. http://eprints.utp.edu.my/19327/
institution Universiti Teknologi Petronas
building UTP Resource Centre
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Petronas
content_source UTP Institutional Repository
url_provider http://eprints.utp.edu.my/
description 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 Π shaped 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.
format Article
author Ahmad, M.
Jung, L.T.
Bhuiyan, A.-A.
spellingShingle Ahmad, M.
Jung, L.T.
Bhuiyan, A.-A.
A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing
author_facet Ahmad, M.
Jung, L.T.
Bhuiyan, A.-A.
author_sort Ahmad, M.
title A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing
title_short A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing
title_full A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing
title_fullStr A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing
title_full_unstemmed A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing
title_sort biological inspired fuzzy adaptive window median filter (fawmf) for enhancing dna signal processing
publisher Elsevier Ireland Ltd
publishDate 2017
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
http://eprints.utp.edu.my/19327/
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score 13.211869

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