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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Updated: Dec 20, 2025

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

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RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition.

Shunfu Mao¹, Lior Pachter², David Tse³

¹Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, United States of America.

|June 3, 2020

Summary

This summary is machine-generated.

RefShannon accurately reconstructs RNA transcripts by leveraging transcript abundance, improving sensitivity in isoform analysis. This novel genome-guided transcriptome assembler enhances RNA-Seq data interpretation.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

RNA sequencing (RNA-Seq) is crucial for gene expression and transcript isoform analysis.
Transcriptome assembly is essential for reconstructing RNA transcripts from short sequencing reads.
Alternative splicing presents challenges for accurate transcriptome assembly.

Purpose of the Study:

To develop a novel genome-guided transcriptome assembler, RefShannon.
To improve the accuracy of transcript reconstruction by exploiting transcript abundance variations.
To enhance sensitivity in isoform-level analysis of RNA transcripts.

Main Methods:

Development of RefShannon, a novel genome-guided transcriptome assembler.
Utilizing varying transcript abundances for accurate reconstruction.
Comparative evaluation against state-of-the-art assemblers.

Main Results:

RefShannon demonstrates improved sensitivity (up to 22%) at a given specificity compared to existing assemblers.
The algorithm effectively reconstructs complex transcript structures arising from alternative splicing.
Successful application in genome-guided transcriptome assembly.

Conclusions:

RefShannon offers enhanced accuracy and sensitivity for isoform-level RNA analysis.
The approach effectively addresses challenges posed by alternative splicing.
RefShannon provides a valuable tool for molecular biology research using RNA-Seq data.