Exploration and retrieval of whole-metagenome sequencing samples
Identifieur interne : 001C58 ( Main/Exploration ); précédent : 001C57; suivant : 001C59Exploration and retrieval of whole-metagenome sequencing samples
Auteurs : Sohan Seth [Finlande] ; Niko V Lim Ki [Finlande] ; Samuel Kaski [Finlande] ; Antti Honkela [Finlande]Source :
- Bioinformatics [ 1367-4803 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- methods : Metagenomics.
- microbiology : Diabetes Mellitus, Type 2, Inflammatory Bowel Diseases.
- Algorithms, Data Mining, High-Throughput Nucleotide Sequencing, Humans, Microbiota, Sequence Analysis, DNA.
Abstract
Url:
DOI: 10.1093/bioinformatics/btu340
PubMed: 24845653
PubMed Central: 4230234
Affiliations:
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Le document en format XML
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<term>Inflammatory Bowel Diseases (microbiology)</term>
<term>Metagenomics (methods)</term>
<term>Microbiota</term>
<term>Sequence Analysis, DNA</term>
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<term>Analyse de séquence d'ADN</term>
<term>Diabète de type 2 (microbiologie)</term>
<term>Fouille de données</term>
<term>Humains</term>
<term>Maladies inflammatoires intestinales (microbiologie)</term>
<term>Microbiote</term>
<term>Métagénomique ()</term>
<term>Séquençage nucléotidique à haut débit</term>
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<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term>
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<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Diabète de type 2</term>
<term>Maladies inflammatoires intestinales</term>
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<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Diabetes Mellitus, Type 2</term>
<term>Inflammatory Bowel Diseases</term>
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<term>Data Mining</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Microbiota</term>
<term>Sequence Analysis, DNA</term>
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<term>Analyse de séquence d'ADN</term>
<term>Fouille de données</term>
<term>Humains</term>
<term>Microbiote</term>
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<front><div type="abstract" xml:lang="en"><p><bold>Motivation:</bold>
Over the recent years, the field of whole-metagenome shotgun sequencing has witnessed significant growth owing to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster and with better coverage than before. This technical advancement has initiated the trend of sequencing multiple samples in different conditions or environments to explore the similarities and dissimilarities of the microbial communities. Examples include the human microbiome project and various studies of the human intestinal tract. With the availability of ever larger databases of such measurements, finding samples similar to a given query sample is becoming a central operation.</p>
<p><bold>Results:</bold>
In this article, we develop a content-based exploration and retrieval method for whole-metagenome sequencing samples. We apply a distributed string mining framework to efficiently extract all informative sequence <italic>k</italic>
-mers from a pool of metagenomic samples and use them to measure the dissimilarity between two samples. We evaluate the performance of the proposed approach on two human gut metagenome datasets as well as human microbiome project metagenomic samples. We observe significant enrichment for diseased gut samples in results of queries with another diseased sample and high accuracy in discriminating between different body sites even though the method is unsupervised.</p>
<p><bold>Availability and implementation:</bold>
A software implementation of the DSM framework is available at <ext-link ext-link-type="uri" xlink:href="https://github.com/HIITMetagenomics/dsm-framework">https://github.com/HIITMetagenomics/dsm-framework</ext-link>
.</p>
<p><bold>Contact:</bold>
<email>sohan.seth@hiit.fi</email>
or <email>antti.honkela@hiit.fi</email>
</p>
<p><bold>Supplementary information:</bold>
<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/lookup/suppl/doi:10.1093/bioinformatics/btu340/-/DC1">Supplementary data</ext-link>
are available at <italic>Bioinformatics</italic>
online.</p>
</div>
</front>
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