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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...
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: May 16, 2026

Cost-Efficient Transcriptomic-Based Drug Screening
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Cost-Efficient Transcriptomic-Based Drug Screening

Published on: February 23, 2024

Transcriptome walking: a laboratory-oriented GUI-based approach to mRNA identification from deep-sequenced data.

Andrew S French1

  • 1Department of Physiology and Biophysics, Dalhousie University, PO BOX 15000, Halifax, NS B3H 4R2, Canada. andrew.french@dal.ca

BMC Research Notes
|December 11, 2012
PubMed
Summary
This summary is machine-generated.

Researchers developed transcriptome walking, a user-friendly method for assembling full mRNA sequences from deep sequencing data. This approach aids in identifying specific gene sequences without extensive bioinformatics knowledge, accelerating biological discovery.

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A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
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A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

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Last Updated: May 16, 2026

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A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
06:34

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

Published on: January 21, 2020

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Deep sequencing generates short RNA sequences, posing challenges for full mRNA assembly, especially with limited genomic data.
  • Current methods often require extensive bioinformatics expertise, limiting accessibility for many researchers.
  • Identifying specific mRNA sequences is crucial for various biological investigations.

Purpose of the Study:

  • To develop a user-friendly method for de novo mRNA sequence assembly from deep sequencing data.
  • To enable rapid identification of specific mRNA molecules without requiring extensive genomic information.
  • To provide a tool accessible to researchers with basic molecular biology and computing skills.

Main Methods:

  • Transcriptome walking: a two-stage approach involving sequence discovery and completion.
  • Utilizes computer-assisted, Graphical User Interface (GUI)-guided user interaction.
  • Iteratively grows sequences by repeated passes through raw deep sequencing data.
  • Integrated software runs on standard computers, leveraging multi-core processors.

Main Results:

  • Successfully assembled complete mRNA sequences, including previously unknown ones in species lacking genomic data.
  • Achieved complete mRNA sequence identification in under 24 hours.
  • The method is accessible to users with limited bioinformatics experience.

Conclusions:

  • Accessible methods for extracting sequence information from deep sequencing data are increasingly important.
  • Transcriptome walking simplifies the process of obtaining complete gene sequences from deep sequencing data.
  • This approach empowers researchers in biological and medical labs to perform advanced transcriptome analysis.