title: CLIPSeqTools--a novel bioinformatics CLIP-seq analysis suite.
abstract: 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.
authors.affiliation: Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Manolis
authors.initials: M
authors.lastname: Maragkakis
authors.affiliation: Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Alexiou
authors.affiliation: Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
authors.forename: Tadashi
authors.initials: T
authors.lastname: Nakaya
authors.affiliation: Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Zissimos
authors.initials: Z
authors.lastname: Mourelatos
mesh_terms: D019295:Computational Biology; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs
keywords: Argonaute; CLIP-seq; HITS-CLIP; RNA binding protein; miRNA