Finding RNA-Protein Interaction Sites Using HMMs.
Sign Up to like & getrecommendations! Published in 2017 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-6753-7_13
Abstract: RNA-binding proteins play important roles in the various stages of RNA maturation through binding to its target RNAs. Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify the targeting sites of… read more here.
Keywords: protein; clip seq; protein interaction; rna binding ... See more keywords
Computational analysis of CLIP-seq data.
Sign Up to like & getrecommendations! Published in 2017 at "Methods"
DOI: 10.1016/j.ymeth.2017.02.006
Abstract: 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,… read more here.
Keywords: clip seq; seq data; computational analysis; binding sites ... See more keywords
Peakhood: individual site context extraction for CLIP-seq peak regions.
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab755
Abstract: MOTIVATION CLIP-seq is by far the most widely used method to determine transcriptome-wide binding sites of RNA-binding proteins (RBPs). The binding site locations are identified from CLIP-seq read data by tools termed peak callers. Many… read more here.
Keywords: clip seq; seq peak; peak regions; seq ... See more keywords
Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding
Sign Up to like & getrecommendations! Published in 2021 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkab198
Abstract: Abstract microRNAs (miRNAs) associate with Ago proteins to post-transcriptionally silence gene expression by targeting mRNAs. To characterize the modes of miRNA-binding, we developed a novel computational framework, called optiCLIP, which considers the reproducibility of the… read more here.
Keywords: clip seq; mode binding; mirna binding; binding sites ... See more keywords