MersV1, Main, Exploration, bibRecord, 001D31

Benchmarking of methods for genomic taxonomy.

Identifieur interne : 001D31 ( Main/Exploration ); précédent : 001D30; suivant : 001D32

Benchmarking of methods for genomic taxonomy.

Auteurs : Mette V. Larsen [Danemark] ; Salvatore Cosentino ; Oksana Lukjancenko ; Dhany Saputra ; Simon Rasmussen ; Henrik Hasman ; Thomas Sicheritz-Pontén ; Frank M. Aarestrup ; David W. Ussery ; Ole Lund

Source :

Journal of clinical microbiology [ 1098-660X ] ; 2014.

RBID : pubmed:24574292

Descripteurs français

KwdFr :
- ADN bactérien (génétique), ARN ribosomique 16S (génétique), Archéobactéries (génétique), Bactéries (génétique), Classification (), Génomique (), Protéines bactériennes (génétique), Référenciation (), Typage par séquençage multilocus ().
MESH :
- génétique : ADN bactérien, ARN ribosomique 16S, Archéobactéries, Bactéries, Protéines bactériennes.
- Classification, Génomique, Référenciation, Typage par séquençage multilocus.

English descriptors

KwdEn :
- Archaea (genetics), Bacteria (genetics), Bacterial Proteins (genetics), Benchmarking (methods), Classification (methods), DNA, Bacterial (genetics), Genomics (methods), Multilocus Sequence Typing (methods), RNA, Ribosomal, 16S (genetics).
MESH :
- chemical , genetics : Bacterial Proteins, DNA, Bacterial, RNA, Ribosomal, 16S.
- genetics : Archaea, Bacteria.
- methods : Benchmarking, Classification, Genomics, Multilocus Sequence Typing.

Abstract

One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is--that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.

DOI: 10.1128/JCM.02981-13
PubMed: 24574292

Affiliations:

Danemark

Le document en format XML

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<front><div type="abstract" xml:lang="en">One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is--that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.</div>
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Benchmarking of methods for genomic taxonomy.

Benchmarking of methods for genomic taxonomy.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

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