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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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RNA Stability01:53

RNA Stability

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Related Experiment Video

Updated: Feb 12, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
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Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

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VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.

MacIntosh Cornwell1, Mahesh Vangala2, Len Taing1,3

  • 1Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.

BMC Bioinformatics
|April 14, 2018
PubMed
Summary
This summary is machine-generated.

A new RNA sequencing analysis pipeline, VIPER, offers a user-friendly solution for researchers. This Visualization Pipeline for RNA-seq analysis simplifies complex data processing, making advanced RNA-seq analysis accessible to non-experts.

Keywords:
AnalysisGene fusionImmunological infiltratePipelineRNA-seqSnakemake

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Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • RNA sequencing (RNA-seq) is a vital tool for quantifying RNA abundance in biological samples.
  • The proliferation of RNA-seq has spurred the development of numerous analysis tools, yet their effective use remains challenging, particularly for non-experts.
  • Scalability and reproducibility are key challenges in RNA sequencing data analysis.

Purpose of the Study:

  • To develop a user-friendly, efficient, and comprehensive pipeline for RNA sequencing analysis.
  • To address the challenges of scalability and reproducibility in RNA-seq data processing.
  • To create a modular pipeline capable of integrating new analysis tools.

Main Methods:

  • Development of the VIPER (Visualization Pipeline for RNA-seq analysis) workflow management system using Snakemake.
  • Integration of popular RNA-seq analysis tools for a complete workflow from raw data to pathway analysis.
  • Modular design allowing for the incorporation of new functionalities, such as immune infiltrate and T-cell CDR reconstruction.

Main Results:

  • VIPER provides a fast, efficient, and comprehensive pipeline for RNA-seq analysis.
  • The pipeline simplifies the process from raw sequencing data through alignment, quality control, differential expression, and pathway analysis.
  • VIPER is packaged for easy installation, requiring minimal computational expertise.

Conclusions:

  • VIPER offers a comprehensive solution for standard RNA-seq analyses.
  • The pipeline is designed for speed, effectiveness, customization, and expansion.
  • VIPER enhances accessibility to advanced RNA-seq analysis for a broader range of researchers.