sRNAtoolbox: an integrated collection of small RNA research tools

Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and plants. MicroRNAs are important in host-microbe interactions and parasite microRNAs might modulate t...

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Main Authors:	Rueda, Antonio, Barturen, Guillermo, Lebrón, Ricardo, Gómez-Martín, Cristina, Alganza, Ángel, Oliver, José L., Hackenberg, Michael
Format:	Online
Language:	English
Published:	Oxford University Press 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489306/

id	pubmed-4489306
recordtype	oai_dc
spelling	pubmed-44893062015-07-07 sRNAtoolbox: an integrated collection of small RNA research tools Rueda, Antonio Barturen, Guillermo Lebrón, Ricardo Gómez-Martín, Cristina Alganza, Ángel Oliver, José L. Hackenberg, Michael Web Server issue Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and plants. MicroRNAs are important in host-microbe interactions and parasite microRNAs might modulate the innate immunity of the host. Furthermore, small RNAs can be detected in bodily fluids making them attractive non-invasive biomarker candidates. Given the general broad interest in small RNAs, and in particular microRNAs, a large number of bioinformatics aided analysis types are needed by the scientific community. To facilitate integrated sRNA research, we developed sRNAtoolbox, a set of independent but interconnected tools for expression profiling from high-throughput sequencing data, consensus differential expression, target gene prediction, visual exploration in a genome context as a function of read length, gene list analysis and blast search of unmapped reads. All tools can be used independently or for the exploration and downstream analysis of sRNAbench results. Workflows like the prediction of consensus target genes of parasite microRNAs in the host followed by the detection of enriched pathways can be easily established. The web-interface interconnecting all these tools is available at http://bioinfo5.ugr.es/srnatoolbox Oxford University Press 2015-07-01 2015-05-27 /pmc/articles/PMC4489306/ /pubmed/26019179 http://dx.doi.org/10.1093/nar/gkv555 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Rueda, Antonio Barturen, Guillermo Lebrón, Ricardo Gómez-Martín, Cristina Alganza, Ángel Oliver, José L. Hackenberg, Michael
spellingShingle	Rueda, Antonio Barturen, Guillermo Lebrón, Ricardo Gómez-Martín, Cristina Alganza, Ángel Oliver, José L. Hackenberg, Michael sRNAtoolbox: an integrated collection of small RNA research tools
author_facet	Rueda, Antonio Barturen, Guillermo Lebrón, Ricardo Gómez-Martín, Cristina Alganza, Ángel Oliver, José L. Hackenberg, Michael
author_sort	Rueda, Antonio
title	sRNAtoolbox: an integrated collection of small RNA research tools
title_short	sRNAtoolbox: an integrated collection of small RNA research tools
title_full	sRNAtoolbox: an integrated collection of small RNA research tools
title_fullStr	sRNAtoolbox: an integrated collection of small RNA research tools
title_full_unstemmed	sRNAtoolbox: an integrated collection of small RNA research tools
title_sort	srnatoolbox: an integrated collection of small rna research tools
description	Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and plants. MicroRNAs are important in host-microbe interactions and parasite microRNAs might modulate the innate immunity of the host. Furthermore, small RNAs can be detected in bodily fluids making them attractive non-invasive biomarker candidates. Given the general broad interest in small RNAs, and in particular microRNAs, a large number of bioinformatics aided analysis types are needed by the scientific community. To facilitate integrated sRNA research, we developed sRNAtoolbox, a set of independent but interconnected tools for expression profiling from high-throughput sequencing data, consensus differential expression, target gene prediction, visual exploration in a genome context as a function of read length, gene list analysis and blast search of unmapped reads. All tools can be used independently or for the exploration and downstream analysis of sRNAbench results. Workflows like the prediction of consensus target genes of parasite microRNAs in the host followed by the detection of enriched pathways can be easily established. The web-interface interconnecting all these tools is available at http://bioinfo5.ugr.es/srnatoolbox
publisher	Oxford University Press
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489306/
_version_	1613243127563288576

sRNAtoolbox: an integrated collection of small RNA research tools

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