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CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.

Identifieur interne : 001619 ( PubMed/Checkpoint ); précédent : 001618; suivant : 001620

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.

Auteurs : Rachid Ounit [États-Unis] ; Steve Wanamaker [États-Unis] ; Timothy J. Close [États-Unis] ; Stefano Lonardi [États-Unis]

Source :

BMC genomics [ 1471-2164 ] ; 2015.

RBID : pubmed:25879410

Descripteurs français

KwdFr :
- Algorithmes, Génomique, Interface utilisateur, Internet, Métagénomique.
MESH :
- Algorithmes, Génomique, Interface utilisateur, Internet, Métagénomique.

English descriptors

KwdEn :
- Algorithms, Genomics, Internet, Metagenomics, User-Computer Interface.
MESH :
- Algorithms, Genomics, Internet, Metagenomics, User-Computer Interface.

Abstract

The problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce.

DOI: 10.1186/s12864-015-1419-2
PubMed: 25879410

Affiliations:

États-Unis

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Le document en format XML

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<front><div type="abstract" xml:lang="en">The problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce.</div>
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<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">We introduce CLARK a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed. Extensive experimental results on various metagenomic samples show that the classification accuracy of CLARK is better or comparable to the best state-of-the-art tools and it is significantly faster than any of its competitors. In its fastest single-threaded mode CLARK classifies, with high accuracy, about 32 million metagenomic short reads per minute. CLARK can also classify BAC clones or transcripts to chromosome arms and centromeric regions.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">CLARK is a versatile, fast and accurate sequence classification method, especially useful for metagenomics and genomics applications. It is freely available at http://clark.cs.ucr.edu/ .</AbstractText>
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CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.

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Abstract

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