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Bioinformatic tools for analysis of CLIP ribonucleoprotein data
Author(s) -
De Supriyo,
Gorospe Myriam
Publication year - 2016
Publication title -
wiley interdisciplinary reviews: rna
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.225
H-Index - 71
eISSN - 1757-7012
pISSN - 1757-7004
DOI - 10.1002/wrna.1404
Subject(s) - ribonucleoprotein , computational biology , computer science , chemistry , microbiology and biotechnology , biology , genetics , rna , gene
Investigating the interactions of RNA ‐binding proteins ( RBPs ) with RNAs is a complex task for molecular and computational biologists. The molecular biology techniques and the computational approaches to understand RBP–RNA (or ribonucleoprotein, RNP ) interactions have advanced considerably over the past few years and numerous and diverse software tools have been developed to analyze these data. Accordingly, laboratories interested in RNP biology face the challenge of choosing adequately among the available software tools those that best address the biological problem they are studying. Here, we focus on state‐of‐the‐art molecular biology techniques that employ crosslinking and immunoprecipitation ( CLIP ) of an RBP to study and map RNP interactions. We review the different software tools and databases available to analyze the most widely used CLIP methods, HITS‐CLIP , PAR‐CLIP , and iCLIP . WIREs RNA 2017, 8:e1404. doi: 10.1002/wrna.1404 This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Evolution and Genomics > Ribonomics RNA Methods > RNA Analyses In Vitro and In Silico