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Related Concept Videos

RNA-seq03:21

RNA-seq

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 microarray-based...
Real Time RT-PCR02:57

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...
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...

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Related Experiment Video

Updated: Jun 12, 2026

AQRNA-seq for Quantifying Small RNAs
05:12

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

rQuant.web: a tool for RNA-Seq-based transcript quantitation.

Regina Bohnert1, Gunnar Rätsch

  • 1Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany. regina.bohnert@tuebingen.mpg.de

Nucleic Acids Research
|June 17, 2010
PubMed
Summary
This summary is machine-generated.

We introduce rQuant.web, a free online tool for RNA sequencing data analysis. This service accurately quantifies RNA transcripts, even alternative ones, by correcting for library preparation, sequencing, and mapping biases.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate quantification of RNA sequencing data is crucial for understanding gene expression.
  • Existing methods may struggle with complex genomic regions, such as multiple transcripts per gene locus.
  • Biases introduced during library preparation, sequencing, and read mapping can affect quantification accuracy.

Purpose of the Study:

  • To present rQuant.web, a novel web service for quantitative analysis of RNA sequencing data.
  • To provide a user-friendly platform for accessing advanced RNA quantification tools.
  • To enable accurate quantification of alternative transcripts.

Main Methods:

  • Development of the rQuant.web service, accessible via a Galaxy installation.
  • Utilizing the rQuant algorithm, which employs quadratic programming for bias estimation.
  • The rQuant algorithm is designed to handle multiple transcripts per gene locus.

Main Results:

  • rQuant.web offers convenient access to quantitative analysis tools for RNA sequencing data.
  • The underlying rQuant technique effectively estimates and corrects for various biases.
  • The method is particularly suitable for quantifying alternative transcripts due to its ability to handle multi-transcript loci.

Conclusions:

  • rQuant.web provides a valuable and accessible resource for researchers analyzing RNA sequencing data.
  • The tool facilitates more accurate transcript quantification, especially for complex transcriptomes.
  • The service is freely available to all users without login requirements, promoting open access to advanced bioinformatics tools.