Cargando…
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...
Autores principales: | , , |
---|---|
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 |
_version_ | 1782222366855659520 |
---|---|
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. |
format | Online Article Text |
id | pubmed-3268242 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT schmiederrobert identificationandremovalofribosomalrnasequencesfrommetatranscriptomes AT limyanwei identificationandremovalofribosomalrnasequencesfrommetatranscriptomes AT edwardsrobert identificationandremovalofribosomalrnasequencesfrommetatranscriptomes |