Cargando…

Classifying the Lifestyle of Metagenomically-Derived Phages Sequences Using Alignment-Free Methods

Phages are viruses that infect bacteria. The phages can be classified into two different categories based on their lifestyles: temperate and lytic. Now, the metavirome can generate a large number of fragments from the viral genomic sequences of entire environmental community, which makes it impossib...

Descripción completa

Detalles Bibliográficos
Autor principal: Song, Kai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7693541/
https://www.ncbi.nlm.nih.gov/pubmed/33304326
http://dx.doi.org/10.3389/fmicb.2020.567769
_version_ 1783614768361242624
author Song, Kai
author_facet Song, Kai
author_sort Song, Kai
collection PubMed
description Phages are viruses that infect bacteria. The phages can be classified into two different categories based on their lifestyles: temperate and lytic. Now, the metavirome can generate a large number of fragments from the viral genomic sequences of entire environmental community, which makes it impossible to determine their lifestyles through experiments. Thus, there is a need to development computational methods for annotating phage contigs and making prediction of their lifestyles. Alignment-based methods for classifying phage lifestyle are limited by incomplete assembled genomes and nucleotide databases. Alignment-free methods based on the frequencies of k-mers were widely used for genome and metagenome comparison which did not rely on the completeness of genome or nucleotide databases. To mimic fragmented metagenomic sequences, the temperate and lytic phages genomic sequences were split into non-overlapping fragments with different lengths, then, I comprehensively compared nine alignment-free dissimilarity measures with a wide range of choices of k-mer length and Markov orders for predicting the lifestyles of these phage contigs. The dissimilarity measure, [Formula: see text] , performed better than other dissimilarity measures for classifying the lifestyles of phages. Thus, I propose that the alignment-free method, [Formula: see text] , can be used for predicting the lifestyles of phages which derived from the metagenomic data.
format Online
Article
Text
id pubmed-7693541
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-76935412020-12-09 Classifying the Lifestyle of Metagenomically-Derived Phages Sequences Using Alignment-Free Methods Song, Kai Front Microbiol Microbiology Phages are viruses that infect bacteria. The phages can be classified into two different categories based on their lifestyles: temperate and lytic. Now, the metavirome can generate a large number of fragments from the viral genomic sequences of entire environmental community, which makes it impossible to determine their lifestyles through experiments. Thus, there is a need to development computational methods for annotating phage contigs and making prediction of their lifestyles. Alignment-based methods for classifying phage lifestyle are limited by incomplete assembled genomes and nucleotide databases. Alignment-free methods based on the frequencies of k-mers were widely used for genome and metagenome comparison which did not rely on the completeness of genome or nucleotide databases. To mimic fragmented metagenomic sequences, the temperate and lytic phages genomic sequences were split into non-overlapping fragments with different lengths, then, I comprehensively compared nine alignment-free dissimilarity measures with a wide range of choices of k-mer length and Markov orders for predicting the lifestyles of these phage contigs. The dissimilarity measure, [Formula: see text] , performed better than other dissimilarity measures for classifying the lifestyles of phages. Thus, I propose that the alignment-free method, [Formula: see text] , can be used for predicting the lifestyles of phages which derived from the metagenomic data. Frontiers Media S.A. 2020-11-12 /pmc/articles/PMC7693541/ /pubmed/33304326 http://dx.doi.org/10.3389/fmicb.2020.567769 Text en Copyright © 2020 Song. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Song, Kai
Classifying the Lifestyle of Metagenomically-Derived Phages Sequences Using Alignment-Free Methods
title Classifying the Lifestyle of Metagenomically-Derived Phages Sequences Using Alignment-Free Methods
title_full Classifying the Lifestyle of Metagenomically-Derived Phages Sequences Using Alignment-Free Methods
title_fullStr Classifying the Lifestyle of Metagenomically-Derived Phages Sequences Using Alignment-Free Methods
title_full_unstemmed Classifying the Lifestyle of Metagenomically-Derived Phages Sequences Using Alignment-Free Methods
title_short Classifying the Lifestyle of Metagenomically-Derived Phages Sequences Using Alignment-Free Methods
title_sort classifying the lifestyle of metagenomically-derived phages sequences using alignment-free methods
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7693541/
https://www.ncbi.nlm.nih.gov/pubmed/33304326
http://dx.doi.org/10.3389/fmicb.2020.567769
work_keys_str_mv AT songkai classifyingthelifestyleofmetagenomicallyderivedphagessequencesusingalignmentfreemethods