Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter

Abstract We describe a novel algorithm for information recovery from DNA sequences by using a digital filter. This work proposes a three-part algorithm to decide the k-mer or q-gram word density. Employing a finite impulse response digital filter, one can calculate the sequence's k-mer or q-gra...

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Autores principales:	Bimal Kumar Sarkar, Ashish Ranjan Sharma, Manojit Bhattacharya, Garima Sharma, Sang-Soo Lee, Chiranjib Chakraborty
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6b477e1a397b4fc8a0a804618f67199d
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spelling	oai:doaj.org-article:6b477e1a397b4fc8a0a804618f67199d2021-12-02T14:33:51ZDetermination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter10.1038/s41598-021-93154-32045-2322https://doaj.org/article/6b477e1a397b4fc8a0a804618f67199d2021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93154-3https://doaj.org/toc/2045-2322Abstract We describe a novel algorithm for information recovery from DNA sequences by using a digital filter. This work proposes a three-part algorithm to decide the k-mer or q-gram word density. Employing a finite impulse response digital filter, one can calculate the sequence's k-mer or q-gram word density. Further principal component analysis is used on word density distribution to analyze the dissimilarity between sequences. A dissimilarity matrix is thus formed and shows the appearance of cluster formation. This cluster formation is constructed based on the alignment-free sequence method. Furthermore, the clusters are used to build phylogenetic relations. The cluster algorithm is in good agreement with alignment-based algorithms. The present algorithm is simple and requires less time for computation than other currently available algorithms. We tested the algorithm using beta hemoglobin coding sequences (HBB) of 10 different species and 18 primate mitochondria genome (mtDNA) sequences.Bimal Kumar SarkarAshish Ranjan SharmaManojit BhattacharyaGarima SharmaSang-Soo LeeChiranjib ChakrabortyNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bimal Kumar Sarkar Ashish Ranjan Sharma Manojit Bhattacharya Garima Sharma Sang-Soo Lee Chiranjib Chakraborty Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter
description	Abstract We describe a novel algorithm for information recovery from DNA sequences by using a digital filter. This work proposes a three-part algorithm to decide the k-mer or q-gram word density. Employing a finite impulse response digital filter, one can calculate the sequence's k-mer or q-gram word density. Further principal component analysis is used on word density distribution to analyze the dissimilarity between sequences. A dissimilarity matrix is thus formed and shows the appearance of cluster formation. This cluster formation is constructed based on the alignment-free sequence method. Furthermore, the clusters are used to build phylogenetic relations. The cluster algorithm is in good agreement with alignment-based algorithms. The present algorithm is simple and requires less time for computation than other currently available algorithms. We tested the algorithm using beta hemoglobin coding sequences (HBB) of 10 different species and 18 primate mitochondria genome (mtDNA) sequences.
format	article
author	Bimal Kumar Sarkar Ashish Ranjan Sharma Manojit Bhattacharya Garima Sharma Sang-Soo Lee Chiranjib Chakraborty
author_facet	Bimal Kumar Sarkar Ashish Ranjan Sharma Manojit Bhattacharya Garima Sharma Sang-Soo Lee Chiranjib Chakraborty
author_sort	Bimal Kumar Sarkar
title	Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter
title_short	Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter
title_full	Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter
title_fullStr	Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter
title_full_unstemmed	Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter
title_sort	determination of k-mer density in a dna sequence and subsequent cluster formation algorithm based on the application of electronic filter
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/6b477e1a397b4fc8a0a804618f67199d
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Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter

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