Computational Methods for CLIP-Seq Data Processing
نویسندگان
چکیده
منابع مشابه
Computational Methods for CLIP-seq Data Processing
RNA-binding proteins (RBPs) are at the core of post-transcriptional regulation and thus of gene expression control at the RNA level. One of the principal challenges in the field of gene expression regulation is to understand RBPs mechanism of action. As a result of recent evolution of experimental techniques, it is now possible to obtain the RNA regions recognized by RBPs on a transcriptome-wid...
متن کاملComputational analysis of CLIP-seq data.
CLIP-seq experiments are currently the most important means for determining the binding sites of RNA binding proteins on a genome-wide level. The computational analysis can be divided into three steps. In the first pre-processing stage, raw reads have to be trimmed and mapped to the genome. This step has to be specifically adapted for each CLIP-seq protocol. The next step is peak calling, which...
متن کاملAssessing Computational Steps for CLIP-Seq Data Analysis
RNA-binding protein (RBP) is a key player in regulating gene expression at the posttranscriptional level. CLIP-Seq, with the ability to provide a genome-wide map of protein-RNA interactions, has been increasingly used to decipher RBP-mediated posttranscriptional regulation. Generating highly reliable binding sites from CLIP-Seq requires not only stringent library preparation but also considerab...
متن کاملCurrent methods in the analysis of CLIP-Seq data
During the process of transcription and post transcription, RNA synthesis and modifications such as alternative splicing is mainly regulated through the binding of functional proteins. Thus, to understand the fate and the molecular function of RNA, one of the key tasks is to map the binding sites between RNA-binding proteins and RNAs[1]. Regard of interactions between RNA and RNA-binding protei...
متن کاملCseq-Simulator: A Data Simulator for CLIP-Seq Experiments
CLIP-Seq protocols such as PAR-CLIP, HITS-CLIP or iCLIP allow a genome-wide analysis of protein-RNA interactions. For the processing of the resulting short read data, various tools are utilized. Some of these tools were specifically developed for CLIP-Seq data, whereas others were designed for the analysis of RNA-Seq data. To this date, however, it has not been assessed which of the available t...
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ژورنال
عنوان ژورنال: Bioinformatics and Biology Insights
سال: 2014
ISSN: 1177-9322,1177-9322
DOI: 10.4137/bbi.s16803