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Identification and removal of ribosomal RNA sequences from metatranscriptomes

Summary: Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular bas...

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Detalles Bibliográficos
Autores principales: Schmieder, Robert, Lim, Yan Wei, Edwards, Robert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268242/
https://www.ncbi.nlm.nih.gov/pubmed/22155869
http://dx.doi.org/10.1093/bioinformatics/btr669
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author Schmieder, Robert
Lim, Yan Wei
Edwards, Robert
author_facet Schmieder, Robert
Lim, Yan Wei
Edwards, Robert
author_sort Schmieder, Robert
collection PubMed
description Summary: Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications. Availability and implementation: This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a user-friendly web interface. The source code, user help and additional information is available at http://ribopicker.sourceforge.net/. Contact: rschmied@sciences.sdsu.edu; rschmied@sciences.sdsu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-32682422012-01-30 Identification and removal of ribosomal RNA sequences from metatranscriptomes Schmieder, Robert Lim, Yan Wei Edwards, Robert Bioinformatics Applications Note Summary: Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications. Availability and implementation: This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a user-friendly web interface. The source code, user help and additional information is available at http://ribopicker.sourceforge.net/. Contact: rschmied@sciences.sdsu.edu; rschmied@sciences.sdsu.edu Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2012-02-01 2011-12-06 /pmc/articles/PMC3268242/ /pubmed/22155869 http://dx.doi.org/10.1093/bioinformatics/btr669 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Schmieder, Robert
Lim, Yan Wei
Edwards, Robert
Identification and removal of ribosomal RNA sequences from metatranscriptomes
title Identification and removal of ribosomal RNA sequences from metatranscriptomes
title_full Identification and removal of ribosomal RNA sequences from metatranscriptomes
title_fullStr Identification and removal of ribosomal RNA sequences from metatranscriptomes
title_full_unstemmed Identification and removal of ribosomal RNA sequences from metatranscriptomes
title_short Identification and removal of ribosomal RNA sequences from metatranscriptomes
title_sort identification and removal of ribosomal rna sequences from metatranscriptomes
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268242/
https://www.ncbi.nlm.nih.gov/pubmed/22155869
http://dx.doi.org/10.1093/bioinformatics/btr669
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