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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...
Tagging and Fusion Proteins01:24

Tagging and Fusion Proteins

Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
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 14, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data.

Wenlong Jia, Kunlong Qiu, Minghui He

    Genome Biology
    |February 16, 2013
    PubMed
    Summary
    This summary is machine-generated.

    We developed SOAPfuse, a new tool for identifying fusion transcripts in RNA sequencing data. This method offers higher efficiency and lower computational cost for detecting novel cancer-related gene fusions.

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    Area of Science:

    • Bioinformatics
    • Genomics
    • Molecular Biology

    Background:

    • Fusion transcripts are critical biomarkers in cancer.
    • Accurate identification of fusion transcripts from RNA-Seq data remains challenging.
    • Existing tools have limitations in efficiency and resource consumption.

    Purpose of the Study:

    • To develop a novel computational method for identifying fusion transcripts.
    • To improve the efficiency and accuracy of fusion transcript detection.
    • To provide a resource for discovering novel fusion events in cancer.

    Main Methods:

    • Development of SOAPfuse, a novel algorithm for fusion transcript identification.
    • Utilized an improved partial exhaustion algorithm to generate fusion junction sequence libraries.
    • Implemented a series of filters for high-confidence fusion transcript nomination.
    • Applied SOAPfuse to paired-end RNA-Seq data from bladder cancer cell lines.

    Main Results:

    • SOAPfuse demonstrated higher detection efficiency compared to existing tools.
    • SOAPfuse required fewer computing resources.
    • Identified 15 fusion transcripts in two bladder cancer cell lines.
    • Discovered several novel fusion events common to both cell lines.

    Conclusions:

    • SOAPfuse is an efficient and resource-conscious tool for fusion transcript identification.
    • The method facilitates the discovery of novel fusion events in cancer.
    • SOAPfuse can aid in the identification of potential cancer biomarkers.