About: Alignment-free method for DNA sequence clustering using Fuzzy integral similarity

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Alignment-free method for DNA sequence clustering using Fuzzy integral similarity Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Alignment-free method for DNA sequence clustering using Fuzzy integral similarity
Creator	Nandi, Soumyadeep Das, Manashi Raj, Garima Saw, Ajay Talukdar, Narayan Tripathy, Chandra
Source	Medline; PMC
abstract	A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence analysis algorithms. In this study, we developed an alignment-free algorithm for faster sequence analysis. The novelty of our approach is the inclusion of fuzzy integral with Markov chain for sequence analysis in the alignment-free model. The method estimate the parameters of a Markov chain by considering the frequencies of occurrence of all possible nucleotide pairs from each DNA sequence. These estimated Markov chain parameters were used to calculate similarity among all pairwise combinations of DNA sequences based on a fuzzy integral algorithm. This matrix is used as an input for the neighbor program in the PHYLIP package for phylogenetic tree construction. Our method was tested on eight benchmark datasets and on in-house generated datasets (18 s rDNA sequences from 11 arbuscular mycorrhizal fungi (AMF) and 16 s rDNA sequences of 40 bacterial isolates from plant interior). The results indicate that the fuzzy integral algorithm is an efficient and feasible alignment-free method for sequence analysis on the genomic scale.
has issue date	2019-03-06(xsd:dateTime)
bibo:doi	10.1038/s41598-019-40452-6
bibo:pmid	30842590
has license	cc-by
sha1sum (hex)	30d216d33a2ead14fe0230f40fd76f6ae2d3b79c
schema:url	https://doi.org/10.1038/s41598-019-40452-6
resource representing a document's title	Alignment-free method for DNA sequence clustering using Fuzzy integral similarity
has PubMed Central identifier	PMC6403383
has PubMed identifier	30842590
schema:publication	Sci Rep
resource representing a document's body	covid:30d216d33a2ead14fe0230f40fd76f6ae2d3b79c#body_text
is schema:about of	named entity '16S RDNA' named entity 'FIGURE' named entity 'MEGA' named entity 'SEQUENCES' named entity 'ISOLATES' named entity 'PACKAGE' named entity 'PHYLOGENETIC TREE' named entity 'SEQUENCE CLUSTERING' named entity 'SIMILARITY' named entity 'BACTERIAL' named entity 'FUZZY' named entity 'INTEGRAL' named entity 'DNA SEQUENCE' named entity 'METHOD' named entity 'FREE' named entity 'ALIGNMENT' named entity 'CONSTRUCTED' named entity 'AMF' named entity 'USING' named entity 'USING' named entity 'CLUSTALW' named entity 'METHOD' named entity 'isolates' named entity 'S17' named entity 'S19' named entity 'Robinson-Foulds' named entity 'Phylogenetic tree' named entity 'Shigella' named entity 'genomes' named entity 'Erinaceomorpha' named entity 'S18' named entity 'Eutherian' named entity 'Phylogenetic tree' named entity 'vector' named entity 'Artiodactyla' named entity 'Carnivore' named entity 'PHYLIP' named entity 'mitochondrial genome' named entity 'Perissodactyla' named entity 'ClustalW' named entity 'mammals' named entity 'mammal' named entity 'Phylogenetic tree' named entity 'ClustalW' named entity 'Cetacea' named entity 'vector' named entity 'mammals' named entity 'S16' named entity 'S15' named entity 'phylogenetic tree' named entity 'Rodentia' named entity 'genome' named entity 'Lagomorpha' named entity 'Primates' named entity 'phylogenetic tree' named entity 'phylogenetic tree' named entity 'ClustalW' named entity 'DNA sequence' named entity '16S rDNA' named entity 'ClustalW' named entity 'phylogenetic tree' named entity 'sequences' named entity 'ClustalW' named entity 'phylogenetic tree' named entity 'bacterial' named entity 'sequences' named entity 'integral' named entity '16S rDNA' named entity 'phylogenetic tree' named entity 'similarity' named entity 'DNA sequence' named entity 'ClustalW' named entity 'Fuzzy'
is part of of	covid:30d216d33a2ead14fe0230f40fd76f6ae2d3b79c#body_text Alignment-free method for DNA sequence clustering using Fuzzy integral similarity A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence analysis algorithms. In this study, we developed an alignment-free algorithm for faster sequence analysis. The novelty of our approach is the inclusion of fuzzy integral with Markov chain for sequence analysis in the alignment-free model. The method estimate the parameters of a Markov chain by considering the frequencies of occurrence of all possible nucleotide pairs from each DNA sequence. These estimated Markov chain parameters were used to calculate similarity among all pairwise combinations of DNA sequences based on a fuzzy integral algorithm. This matrix is used as an input for the neighbor program in the PHYLIP package for phylogenetic tree construction. Our method was tested on eight benchmark datasets and on in-house generated datasets (18 s rDNA sequences from 11 arbuscular mycorrhizal fungi (AMF) and 16 s rDNA sequences of 40 bacterial isolates from plant interior). The results indicate that the fuzzy integral algorithm is an efficient and feasible alignment-free method for sequence analysis on the genomic scale.

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software