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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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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

BSXplorer: analytical framework for exploratory analysis of BS-seq data.

Konstantin Yuditskiy¹, Igor Bezdvornykh¹, Anastasiya Kazantseva²

¹Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia, 199004.

BMC Bioinformatics

|March 4, 2024

Summary

BSXplorer offers a new tool for visualizing DNA methylation patterns from bisulfite sequencing data. This aids in analyzing epigenetic regulation, especially in non-model organisms for evolutionary and agrigenomics research.

Keywords:

Bisulfite sequencing Clustering DNA methylation Epigenomics Exploratory data analysis and visualization Gene body methylation Gene modules Methylation density Non-model organisms

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Last Updated: Jul 1, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Published on: October 5, 2018

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Published on: June 15, 2018

Area of Science:

Epigenetics
Genomics
Bioinformatics

Background:

Bisulfite sequencing is key for understanding DNA methylation, gene expression, and phenotypic variation.
Visualizing genome-wide methylation data is critical, particularly for non-model organisms with limited genomic resources.
Existing tools for graphical analysis of bisulfite sequencing data are limited, hindering evolutionary and agrigenomics studies.

Purpose of the Study:

To introduce BSXplorer, a novel tool designed for efficient graphical analysis of bisulfite sequencing data.
To address the need for user-friendly and robust standalone tools for exploring DNA methylation patterns in non-model systems.

Main Methods:

BSXplorer provides graphical analysis including line plots, heatmaps, and summary statistics for methylation levels.
The tool enables comparative analyses of methylation patterns across samples, contexts, and species.
It facilitates the identification of genomic modules with similar methylation signatures.

Main Results:

BSXplorer offers in-depth graphical analysis of bisulfite sequencing data.
The tool supports comparative analyses and identification of methylation pattern modules.
It processes data rapidly and generates publication-quality figures, with API and CLI options.

Conclusions:

BSXplorer simplifies methylation data mining, comparison, and visualization.
This package is a valuable, easy-to-use resource for epigenetic research.