PARma: identification of microRNA target sites in AGO-PAR-CLIP data

PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iterativel...

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Detalles Bibliográficos
Autores principales: Erhard, Florian, Dölken, Lars, Jaskiewicz, Lukasz, Zimmer, Ralf
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054675/
https://www.ncbi.nlm.nih.gov/pubmed/23895117
http://dx.doi.org/10.1186/gb-2013-14-7-r79
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author Erhard, Florian
Dölken, Lars
Jaskiewicz, Lukasz
Zimmer, Ralf
author_facet Erhard, Florian
Dölken, Lars
Jaskiewicz, Lukasz
Zimmer, Ralf
author_sort Erhard, Florian
collection PubMed
description PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma
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spelling pubmed-40546752014-06-12 PARma: identification of microRNA target sites in AGO-PAR-CLIP data Erhard, Florian Dölken, Lars Jaskiewicz, Lukasz Zimmer, Ralf Genome Biol Software PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma BioMed Central 2013 2013-07-29 /pmc/articles/PMC4054675/ /pubmed/23895117 http://dx.doi.org/10.1186/gb-2013-14-7-r79 Text en Copyright © 2013 Erhard et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Erhard, Florian
Dölken, Lars
Jaskiewicz, Lukasz
Zimmer, Ralf
PARma: identification of microRNA target sites in AGO-PAR-CLIP data
title PARma: identification of microRNA target sites in AGO-PAR-CLIP data
title_full PARma: identification of microRNA target sites in AGO-PAR-CLIP data
title_fullStr PARma: identification of microRNA target sites in AGO-PAR-CLIP data
title_full_unstemmed PARma: identification of microRNA target sites in AGO-PAR-CLIP data
title_short PARma: identification of microRNA target sites in AGO-PAR-CLIP data
title_sort parma: identification of microrna target sites in ago-par-clip data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054675/
https://www.ncbi.nlm.nih.gov/pubmed/23895117
http://dx.doi.org/10.1186/gb-2013-14-7-r79
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AT jaskiewiczlukasz parmaidentificationofmicrornatargetsitesinagoparclipdata
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