Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.

Information theoretic approaches are ubiquitous and effective in a wide variety of bioinformatics applications. In comparative genomics, alignment-free methods, based on short DNA words, or k-mers, are particularly powerful. We evaluated the utility of varying k-mer lengths for genome comparisons by...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Yuval Bussi, Ruti Kapon, Ziv Reich
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/245f2896b0d84253a7e346dc3bf9ac4d
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:245f2896b0d84253a7e346dc3bf9ac4d
record_format	dspace
spelling	oai:doaj.org-article:245f2896b0d84253a7e346dc3bf9ac4d2021-12-02T20:16:55ZLarge-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.1932-620310.1371/journal.pone.0258693https://doaj.org/article/245f2896b0d84253a7e346dc3bf9ac4d2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0258693https://doaj.org/toc/1932-6203Information theoretic approaches are ubiquitous and effective in a wide variety of bioinformatics applications. In comparative genomics, alignment-free methods, based on short DNA words, or k-mers, are particularly powerful. We evaluated the utility of varying k-mer lengths for genome comparisons by analyzing their sequence space coverage of 5805 genomes in the KEGG GENOME database. In subsequent analyses on four k-mer lengths spanning the relevant range (11, 21, 31, 41), hierarchical clustering of 1634 genus-level representative genomes using pairwise 21- and 31-mer Jaccard similarities best recapitulated a phylogenetic/taxonomic tree of life with clear boundaries for superkingdom domains and high subtree similarity for named taxons at lower levels (family through phylum). By analyzing ~14.2M prokaryotic genome comparisons by their lowest-common-ancestor taxon levels, we detected many potential misclassification errors in a curated database, further demonstrating the need for wide-scale adoption of quantitative taxonomic classifications based on whole-genome similarity.Yuval BussiRuti KaponZiv ReichPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10, p e0258693 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yuval Bussi Ruti Kapon Ziv Reich Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.
description	Information theoretic approaches are ubiquitous and effective in a wide variety of bioinformatics applications. In comparative genomics, alignment-free methods, based on short DNA words, or k-mers, are particularly powerful. We evaluated the utility of varying k-mer lengths for genome comparisons by analyzing their sequence space coverage of 5805 genomes in the KEGG GENOME database. In subsequent analyses on four k-mer lengths spanning the relevant range (11, 21, 31, 41), hierarchical clustering of 1634 genus-level representative genomes using pairwise 21- and 31-mer Jaccard similarities best recapitulated a phylogenetic/taxonomic tree of life with clear boundaries for superkingdom domains and high subtree similarity for named taxons at lower levels (family through phylum). By analyzing ~14.2M prokaryotic genome comparisons by their lowest-common-ancestor taxon levels, we detected many potential misclassification errors in a curated database, further demonstrating the need for wide-scale adoption of quantitative taxonomic classifications based on whole-genome similarity.
format	article
author	Yuval Bussi Ruti Kapon Ziv Reich
author_facet	Yuval Bussi Ruti Kapon Ziv Reich
author_sort	Yuval Bussi
title	Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.
title_short	Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.
title_full	Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.
title_fullStr	Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.
title_full_unstemmed	Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.
title_sort	large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/245f2896b0d84253a7e346dc3bf9ac4d
work_keys_str_mv	AT yuvalbussi largescalekmerbasedanalysisoftheinformationalpropertiesofgenomescomparativegenomicsandtaxonomy AT rutikapon largescalekmerbasedanalysisoftheinformationalpropertiesofgenomescomparativegenomicsandtaxonomy AT zivreich largescalekmerbasedanalysisoftheinformationalpropertiesofgenomescomparativegenomicsandtaxonomy
_version_	1718374393166430208

Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy.

Ejemplares similares