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CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite

Immunoprecipitation of RNA binding proteins (RBPs) after in vivo crosslinking, coupled with sequencing of associated RNA footprints (HITS-CLIP, CLIP-seq), is a method of choice for the identification of RNA targets and binding sites for RBPs. Compared with RNA-seq, CLIP-seq analysis is widely divers...

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Detalles Bibliográficos
Autores principales: Maragkakis, Manolis, Alexiou, Panagiotis, Nakaya, Tadashi, Mourelatos, Zissimos
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691824/
https://www.ncbi.nlm.nih.gov/pubmed/26577377
http://dx.doi.org/10.1261/rna.052167.115
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author Maragkakis, Manolis
Alexiou, Panagiotis
Nakaya, Tadashi
Mourelatos, Zissimos
author_facet Maragkakis, Manolis
Alexiou, Panagiotis
Nakaya, Tadashi
Mourelatos, Zissimos
author_sort Maragkakis, Manolis
collection PubMed
description Immunoprecipitation of RNA binding proteins (RBPs) after in vivo crosslinking, coupled with sequencing of associated RNA footprints (HITS-CLIP, CLIP-seq), is a method of choice for the identification of RNA targets and binding sites for RBPs. Compared with RNA-seq, CLIP-seq analysis is widely diverse and depending on the RBPs that are analyzed, the approaches vary significantly, necessitating the development of flexible and efficient informatics tools. In this study, we present CLIPSeqTools, a novel, highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. It contains a wide array of tools to provide an in-depth view of CLIP-seq data sets. It supports extensive customization and promotes improvization, a critical virtue, since CLIP-seq analysis is rarely well defined a priori. To highlight CLIPSeqTools capabilities, we used the suite to analyze Ago-miRNA HITS-CLIP data sets that we prepared from human brains.
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spelling pubmed-46918242017-01-01 CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite Maragkakis, Manolis Alexiou, Panagiotis Nakaya, Tadashi Mourelatos, Zissimos RNA Bioinformatics Immunoprecipitation of RNA binding proteins (RBPs) after in vivo crosslinking, coupled with sequencing of associated RNA footprints (HITS-CLIP, CLIP-seq), is a method of choice for the identification of RNA targets and binding sites for RBPs. Compared with RNA-seq, CLIP-seq analysis is widely diverse and depending on the RBPs that are analyzed, the approaches vary significantly, necessitating the development of flexible and efficient informatics tools. In this study, we present CLIPSeqTools, a novel, highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. It contains a wide array of tools to provide an in-depth view of CLIP-seq data sets. It supports extensive customization and promotes improvization, a critical virtue, since CLIP-seq analysis is rarely well defined a priori. To highlight CLIPSeqTools capabilities, we used the suite to analyze Ago-miRNA HITS-CLIP data sets that we prepared from human brains. Cold Spring Harbor Laboratory Press 2016-01 /pmc/articles/PMC4691824/ /pubmed/26577377 http://dx.doi.org/10.1261/rna.052167.115 Text en © 2015 Maragkakis et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Bioinformatics
Maragkakis, Manolis
Alexiou, Panagiotis
Nakaya, Tadashi
Mourelatos, Zissimos
CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite
title CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite
title_full CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite
title_fullStr CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite
title_full_unstemmed CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite
title_short CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite
title_sort clipseqtools—a novel bioinformatics clip-seq analysis suite
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691824/
https://www.ncbi.nlm.nih.gov/pubmed/26577377
http://dx.doi.org/10.1261/rna.052167.115
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