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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...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2020
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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 |
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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 |