OptiFit: an Improved Method for Fitting Amplicon Sequences to Existing OTUs.

Cluster Analysis Metagenomics / methods Phylogeny RNA, Ribosomal, 16S / genetics Sequence Analysis, DNA / methods
16S rRNA gene bioinformatics clustering metagenomics microbial ecology microbiome

Journal

mSphere
ISSN: 2379-5042
Titre abrégé: mSphere
Pays: United States
ID NLM: 101674533

Informations de publication

Date de publication:
23 02 2022
Historique:
pubmed: 3 2 2022
medline: 27 4 2022
entrez: 2 2 2022
Statut: ppublish

Résumé

Assigning amplicon sequences to operational taxonomic units (OTUs) is an important step in characterizing microbial communities across large data sets. A notable difference between

Identifiants

DOI: 10.1128/msphere.00916-21 PMID: 35107341 PMC: PMC8809378
pubmed: 35107341
doi: 10.1128/msphere.00916-21
pmc: PMC8809378
doi:

Substances chimiques

RNA, Ribosomal, 16S 0

Types de publication

Journal Article Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

e0091621

Subventions

Organisme : NCI NIH HHS
ID : R01 CA215574
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG000040
Pays : United States
Organisme : NIAID NIH HHS
ID : U01 AI124255
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM070449
Pays : United States
Organisme : NCI NIH HHS
ID : T32 CA140044
Pays : United States

Références

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pubmed: 23793624
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pubmed: 24060131
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pubmed: 22688727
mSystems. 2016 Apr 26;1(2):
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pubmed: 19801464
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pubmed: 32939066
PeerJ. 2015 Dec 08;3:e1487
pubmed: 26664811
mSphere. 2017 Mar 8;2(2):
pubmed: 28289728
Appl Environ Microbiol. 2006 Jul;72(7):5069-72
pubmed: 16820507
Bioinformatics. 2012 Oct 1;28(19):2520-2
pubmed: 22908215
Bioinformatics. 2010 Oct 1;26(19):2460-1
pubmed: 20709691
Front Microbiol. 2016 Apr 25;7:579
pubmed: 27199914
Genome Med. 2016 Apr 06;8(1):37
pubmed: 27056827
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
PeerJ. 2016 Oct 18;4:e2584
pubmed: 27781170
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pubmed: 24288368
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pubmed: 31341288
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pubmed: 27303734
Bioinformatics. 2011 Aug 15;27(16):2194-200
pubmed: 21700674

Auteurs

Kelly L Sovacool (KL)

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
ORCID: 0000-0003-3283-829X

Sarah L Westcott (SL)

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.

M Brodie Mumphrey (MB)

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
ORCID: 0000-0003-3150-8694

Gabrielle A Dotson (GA)

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
ORCID: 0000-0001-6624-5332

Patrick D Schloss (PD)

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.
Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
ORCID: 0000-0002-6935-4275

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Classifications MeSH

questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Statistiques comme sujet › Analyse de regroupements › OptiFit: an Improved Method for Fitting...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Métagénomique › OptiFit: an Improved Method for Fitting...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › OptiFit: an Improved Method for Fitting...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN ribosomique › ARN ribosomique 16S › OptiFit: an Improved Method for Fitting...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › OptiFit: an Improved Method for Fitting...