Rapid alignment-free phylogenetic identification of metagenomic sequences.
Identifieur interne : 000409 ( PubMed/Checkpoint ); précédent : 000408; suivant : 000410Rapid alignment-free phylogenetic identification of metagenomic sequences.
Auteurs : Benjamin Linard [France] ; Krister Swenson [France] ; Fabio Pardi [France]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2019.
Abstract
Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However, likelihood-based PP algorithms struggle to scale with the ever-increasing throughput of DNA sequencing.
DOI: 10.1093/bioinformatics/btz068
PubMed: 30698645
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:30698645Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Rapid alignment-free phylogenetic identification of metagenomic sequences.</title><author><name sortKey="Linard, Benjamin" sort="Linard, Benjamin" uniqKey="Linard B" first="Benjamin" last="Linard">Benjamin Linard</name><affiliation wicri:level="3"><nlm:affiliation>LIRMM, University of Montpellier, CNRS, Montpellier, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>LIRMM, University of Montpellier, CNRS, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Swenson, Krister" sort="Swenson, Krister" uniqKey="Swenson K" first="Krister" last="Swenson">Krister Swenson</name><affiliation wicri:level="3"><nlm:affiliation>LIRMM, University of Montpellier, CNRS, Montpellier, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>LIRMM, University of Montpellier, CNRS, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Pardi, Fabio" sort="Pardi, Fabio" uniqKey="Pardi F" first="Fabio" last="Pardi">Fabio Pardi</name><affiliation wicri:level="3"><nlm:affiliation>LIRMM, University of Montpellier, CNRS, Montpellier, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>LIRMM, University of Montpellier, CNRS, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30698645</idno><idno type="pmid">30698645</idno><idno type="doi">10.1093/bioinformatics/btz068</idno><idno type="wicri:Area/PubMed/Corpus">000654</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000654</idno><idno type="wicri:Area/PubMed/Curation">000654</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000654</idno><idno type="wicri:Area/PubMed/Checkpoint">000409</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000409</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Rapid alignment-free phylogenetic identification of metagenomic sequences.</title><author><name sortKey="Linard, Benjamin" sort="Linard, Benjamin" uniqKey="Linard B" first="Benjamin" last="Linard">Benjamin Linard</name><affiliation wicri:level="3"><nlm:affiliation>LIRMM, University of Montpellier, CNRS, Montpellier, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>LIRMM, University of Montpellier, CNRS, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Swenson, Krister" sort="Swenson, Krister" uniqKey="Swenson K" first="Krister" last="Swenson">Krister Swenson</name><affiliation wicri:level="3"><nlm:affiliation>LIRMM, University of Montpellier, CNRS, Montpellier, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>LIRMM, University of Montpellier, CNRS, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author><author><name sortKey="Pardi, Fabio" sort="Pardi, Fabio" uniqKey="Pardi F" first="Fabio" last="Pardi">Fabio Pardi</name><affiliation wicri:level="3"><nlm:affiliation>LIRMM, University of Montpellier, CNRS, Montpellier, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>LIRMM, University of Montpellier, CNRS, Montpellier</wicri:regionArea><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However, likelihood-based PP algorithms struggle to scale with the ever-increasing throughput of DNA sequencing.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">30698645</PMID><DateRevised><Year>2019</Year><Month>09</Month><Day>18</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>35</Volume><Issue>18</Issue><PubDate><Year>2019</Year><Month>Sep</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Rapid alignment-free phylogenetic identification of metagenomic sequences.</ArticleTitle><Pagination><MedlinePgn>3303-3312</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btz068</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However, likelihood-based PP algorithms struggle to scale with the ever-increasing throughput of DNA sequencing.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We have developed RAPPAS (Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences) which uses an alignment-free approach, removing the hurdle of query sequence alignment as a preliminary step to PP. Our approach relies on the precomputation of a database of k-mers that may be present with non-negligible probability in relatives of the reference sequences. The placement is performed by inspecting the stored phylogenetic origins of the k-mers in the query, and their probabilities. The database can be reused for the analysis of several different metagenomes. Experiments show that the first implementation of RAPPAS is already faster than competing likelihood-based PP algorithms, while keeping similar accuracy for short reads. RAPPAS scales PP for the era of routine metagenomic diagnostics.</AbstractText><AbstractText Label="AVAILABILITY AND IMPLEMENTATION" NlmCategory="METHODS">Program and sources freely available for download at https://github.com/blinard-BIOINFO/RAPPAS.</AbstractText><AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText><CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Linard</LastName><ForeName>Benjamin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>LIRMM, University of Montpellier, CNRS, Montpellier, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>ISEM, University of Montpellier, CNRS, IRD, EPHE, CIRAD, INRAP, Montpellier, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>AGAP, University of Montpellier, CIRAD, INRA, Montpellier Supagro, Montpellier, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Swenson</LastName><ForeName>Krister</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>LIRMM, University of Montpellier, CNRS, Montpellier, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institut de Biologie Computationnelle, Montpellier, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pardi</LastName><ForeName>Fabio</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>LIRMM, University of Montpellier, CNRS, Montpellier, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institut de Biologie Computationnelle, Montpellier, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>06</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>01</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>01</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>1</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>1</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>1</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30698645</ArticleId><ArticleId IdType="pii">5303992</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btz068</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Languedoc-Roussillon</li><li>Occitanie (région administrative)</li></region><settlement><li>Montpellier</li></settlement></list><tree><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Linard, Benjamin" sort="Linard, Benjamin" uniqKey="Linard B" first="Benjamin" last="Linard">Benjamin Linard</name></region><name sortKey="Pardi, Fabio" sort="Pardi, Fabio" uniqKey="Pardi F" first="Fabio" last="Pardi">Fabio Pardi</name><name sortKey="Swenson, Krister" sort="Swenson, Krister" uniqKey="Swenson K" first="Krister" last="Swenson">Krister Swenson</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000409 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd -nk 000409 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Checkpoint
|type= RBID
|clé= pubmed:30698645
|texte= Rapid alignment-free phylogenetic identification of metagenomic sequences.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:30698645" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |