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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...

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Updated: May 15, 2026

Computational Analysis Tutorial for Chimeric Small Noncoding RNA: Target RNA Sequencing Libraries
07:35

Computational Analysis Tutorial for Chimeric Small Noncoding RNA: Target RNA Sequencing Libraries

Published on: December 1, 2023

scRAPID-web: a web server for predicting protein-RNA interactions from single-cell transcriptomics.

Jonathan Fiorentino1, Alexandros Armaos2, Chiara Montrone1,3

  • 1Center for Life Nano- and Neuro-Science, RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, 00161, Italy.

BMC Genomics
|May 14, 2026
PubMed
Summary
This summary is machine-generated.

scRAPID-web provides a user-friendly platform for analyzing single-cell RNA sequencing data to predict RNA-binding protein (RBP) interactions. This tool enhances understanding of gene regulation by identifying key RBPs and their RNA targets.

Keywords:
Gene regulatory networkLong non-coding RNAProtein–RNA interactionRNA-binding proteinSingle-cell transcriptomicsWeb server

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Area of Science:

  • Computational biology
  • Genomics
  • Bioinformatics

Background:

  • Single-cell RNA sequencing (scRNA-seq) offers high-resolution gene expression analysis at the cellular level.
  • Previous work established scRAPID, a pipeline for predicting RNA-binding protein (RBP)-RNA interactions and identifying hub RBPs using gene regulatory network (GRN) inference and catRAPID.
  • scRAPID-web is introduced to broaden access to these analyses.

Purpose of the Study:

  • To develop a user-friendly web server (scRAPID-web) for predicting RBP-RNA and RBP-RBP interactions.
  • To enable analysis of scRNA-seq data across eight model organisms.
  • To democratize access to GRN-based analyses for RBP-RNA interactions.

Main Methods:

  • scRAPID-web incorporates customizable preprocessing options for scRNA-seq data, including gene selection and cell type filtering.
  • Users can select from three GRN inference algorithms and specify analysis focus on particular gene types.
  • The platform includes precompiled libraries for efficient filtering and motif-based validation of inferred interactions.

Main Results:

  • scRAPID-web generates detailed tables of predicted protein-RNA pairs and hub proteins.
  • Interactive network visualizations display potential RBP complexes based on shared target analysis.
  • The server facilitates prediction of RBP-RNA and RBP-RBP interactions from scRNA-seq data.

Conclusions:

  • scRAPID-web democratizes GRN-based analysis of gene regulation from scRNA-seq data.
  • The tool provides insights into RBP-RNA interactions and regulatory complexes.
  • scRAPID-web is freely accessible, supporting broader research in gene regulation.