Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Application of database-independent approach to assess the quality of OTU picking methods

View ORCID ProfilePatrick D. Schloss
doi: https://doi.org/10.1101/042812
Patrick D. Schloss
Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Patrick D. Schloss
  • For correspondence: pschloss@umich.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Assigning 16S rRNA gene sequences to operational taxonomic units (OTUs) allows microbial ecologists to overcome the inconsistencies and biases within bacterial taxonomy and provides a strategy for clustering similar sequences that do not have representatives in a reference database. I have applied the Matthew’s correlation coefficient to assess the ability of 15 reference-independent and-dependent clustering algorithms to assign sequences to OTUs. This metric quantifies the ability of an algorithm to reflect the relationships between sequences without the use of a reference and can be applied to any dataset or method. The most consistently robust method was the average neighbor algorithm; however, for some datasets other algorithms matched its performance.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted March 08, 2016.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Application of database-independent approach to assess the quality of OTU picking methods
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Application of database-independent approach to assess the quality of OTU picking methods
Patrick D. Schloss
bioRxiv 042812; doi: https://doi.org/10.1101/042812
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Application of database-independent approach to assess the quality of OTU picking methods
Patrick D. Schloss
bioRxiv 042812; doi: https://doi.org/10.1101/042812

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3502)
  • Biochemistry (7343)
  • Bioengineering (5319)
  • Bioinformatics (20258)
  • Biophysics (10008)
  • Cancer Biology (7735)
  • Cell Biology (11293)
  • Clinical Trials (138)
  • Developmental Biology (6434)
  • Ecology (9947)
  • Epidemiology (2065)
  • Evolutionary Biology (13315)
  • Genetics (9359)
  • Genomics (12579)
  • Immunology (7696)
  • Microbiology (19008)
  • Molecular Biology (7437)
  • Neuroscience (41011)
  • Paleontology (300)
  • Pathology (1228)
  • Pharmacology and Toxicology (2134)
  • Physiology (3155)
  • Plant Biology (6858)
  • Scientific Communication and Education (1272)
  • Synthetic Biology (1895)
  • Systems Biology (5311)
  • Zoology (1087)