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RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys

BACKGROUND: Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences a...

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Autores principales: Xie, Chao, Goi, Chin Lui Wesley, Huson, Daniel H., Little, Peter F. R., Williams, Rohan B. H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259810/
https://www.ncbi.nlm.nih.gov/pubmed/28155666
http://dx.doi.org/10.1186/s12859-016-1378-x
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author Xie, Chao
Goi, Chin Lui Wesley
Huson, Daniel H.
Little, Peter F. R.
Williams, Rohan B. H.
author_facet Xie, Chao
Goi, Chin Lui Wesley
Huson, Daniel H.
Little, Peter F. R.
Williams, Rohan B. H.
author_sort Xie, Chao
collection PubMed
description BACKGROUND: Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis. RESULTS: Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion. CONCLUSIONS: RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs.
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spelling pubmed-52598102017-01-26 RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys Xie, Chao Goi, Chin Lui Wesley Huson, Daniel H. Little, Peter F. R. Williams, Rohan B. H. BMC Bioinformatics Software BACKGROUND: Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis. RESULTS: Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion. CONCLUSIONS: RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs. BioMed Central 2016-12-22 /pmc/articles/PMC5259810/ /pubmed/28155666 http://dx.doi.org/10.1186/s12859-016-1378-x Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Xie, Chao
Goi, Chin Lui Wesley
Huson, Daniel H.
Little, Peter F. R.
Williams, Rohan B. H.
RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
title RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
title_full RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
title_fullStr RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
title_full_unstemmed RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
title_short RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
title_sort ribotagger: fast and unbiased 16s/18s profiling using whole community shotgun metagenomic or metatranscriptome surveys
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259810/
https://www.ncbi.nlm.nih.gov/pubmed/28155666
http://dx.doi.org/10.1186/s12859-016-1378-x
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