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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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Viruses with RNA Genomes01:29

Viruses with RNA Genomes

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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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Transcription Elongation Factors02:35

Transcription Elongation Factors

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Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA...
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Transcription01:10

Transcription

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Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
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Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

27.1K
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
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Prokaryotic Transcriptional Activators and Repressors01:58

Prokaryotic Transcriptional Activators and Repressors

25.5K
The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...
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Related Experiment Video

Updated: Feb 5, 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

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TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data.

Readman Chiu1, Ka Ming Nip1, Justin Chu1

  • 1Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 100-570 West 7th Ave, Vancouver, BC, V5Z 4S6, Canada.

BMC Medical Genomics
|September 12, 2018
PubMed
Summary
This summary is machine-generated.

We developed a fast Targeted Assembly Pipeline (TAP) for RNA-sequencing (RNA-seq) data analysis, significantly reducing turnaround time for clinical molecular diagnostics. TAP accurately detects gene fusions and splicing variants in cancer samples.

Keywords:
Acute myeloid leukemiaAlternative splicingClinical genomicsGene fusionInternal tandem duplicationPartial tandem duplicationRNA-seqTranscriptome assembly

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Diagnostics

Background:

  • RNA-sequencing (RNA-seq) is crucial for molecular diagnostics but clinical adoption is hindered by long analysis times.
  • Short-read transcriptome assembly remains valuable for identifying transcript-level alterations.
  • Existing de novo assembly methods face challenges in clinical turnaround times.

Purpose of the Study:

  • To develop a targeted approach to expedite RNA-seq data assembly and analysis for clinical applications.
  • To create a robust pipeline for detecting molecular anomalies in cancer diagnostics.

Main Methods:

  • The Targeted Assembly Pipeline (TAP) integrates alignment-free read classification (BioBloomTools), targeted de novo assembly (Trans-ABySS), read alignment (GMAP, BWA), and variant detection (PAVFinder).
  • PAVFinder was validated for gene fusion detection against established tools using simulated data.
  • TAP was applied to acute myeloid leukemia (AML) RNA-seq data targeting 580 COSMIC genes.

Main Results:

  • PAVFinder demonstrated robust gene fusion detection capabilities.
  • TAP successfully identified diverse molecular anomalies in AML samples, including gene fusions, tandem duplications, insertions, and deletions, consistent with published findings.
  • The pipeline also detected AML-specific splicing variants, such as skipped exons and novel splice sites.
  • TAP processed 100-150 million read pairs for a 580-gene set in 1-2 hours on a 48-core machine.

Conclusions:

  • The Targeted Assembly Pipeline (TAP) is a fast and robust RNA-seq variant detection tool.
  • TAP shows potential for clinical applications in molecular diagnostics due to its speed and accuracy.
  • The TAP software is publicly available for research and clinical use.