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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. 
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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.
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Related Experiment Video

Updated: Apr 17, 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

553

IAOseq: inferring abundance of overlapping genes using RNA-seq data.

Hong Sun, Shuang Yang, Liangliang Tun

    BMC Bioinformatics
    |February 25, 2015
    PubMed
    Summary

    A new tool, IAOseq, accurately quantifies overlapping gene expression from RNA-seq data. It overcomes limitations in high-throughput analysis, improving understanding of gene regulation by overlapping transcripts.

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    Area of Science:

    • Genomics
    • Gene Expression Analysis

    Background:

    • Overlapping transcription is a key gene expression regulator.
    • Existing assays lack high-throughput expression data for overlapping transcripts.

    Purpose of the Study:

    • To develop a high-throughput tool for analyzing overlapping transcription.
    • To improve the accuracy of quantifying overlapping gene expression.

    Main Methods:

    • Developed IAOseq, a tool utilizing read distribution along transcribed regions.
    • Analyzed standard RNA-seq data to identify overlapping gene expression levels.

    Main Results:

    • IAOseq demonstrated superior accuracy in estimating overlapping transcription levels compared to five existing methods.
    • IAOseq identified a 1.6-fold overestimation of same-strand overlapping gene expression by commonly used methods.
    • Distinguished expression from different mRNA strands in same-strand overlapping transcription.

    Conclusions:

    • IAOseq provides a valuable tool for analyzing overlapping transcription from standard RNA-seq libraries.
    • Facilitates understanding of regulatory mechanisms involving overlapping transcripts.
    • IAOseq is freely accessible for research use.