GenomeVisualizer 0.0.1

A toolbox for detecting DNA replication origins and regulatory motifs in genomic sequences

GenomeVisualizer - A toolbox for detecting DNA replication origins and regulatory motifs in genomic sequences

A toolbox for detecting DNA replication origins and regulatory motifs in genomic sequences. The toolbox includes modules for skew analysis, origin prediction, motif search, and graphical genome representation.

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Current Version: 0.0.1

Planned Release: June 2025

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Introduction

GenomeVisualizer was developed to support students, researchers, and enthusiasts in exploring the structure of prokaryotic genomes.
It provides tools to identify biologically significant regions such as replication origins (ori) and sequence motifs associated with regulatory processes like circadian rhythms.

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Description

The toolbox is divided into the following modules:

• Basic:

  • Simple pattern counting, frequency mapping, and file loading utilities.

• Replication:

  • Tools to locate replication origin using GC-skew, Hamming distance, and approximate pattern matching.

• Motifs:

  • Motif search algorithms including Greedy Motif Search and Gibbs Sampling.

• Visualization:

  • Genome-wide plots for skew array, symbol distribution, and motif locations using matplotlib.

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For more information, visit the official documentation.

Installation

From PyPi

Install GenomeVisualizer using pip

pip install GenomeVisualizer

From source

Clone the git repository

git clone "https://github.com/vargaheni05/GenomeVisualizer.git"

Change directory to the cloned repository

cd GenomeVisualizer/Toolbox

Install with pip

pip install .

Building the documentation

Install required packages

pip install -r docs/requirements.txt

Call Sphinx build command

sphinx-build -M html docs/source docs/build

On Windows you can also run the make.bat file

.\docs\make.bat html

The documentation should be available in the docs/build directory as html files
This includes the example codes as tutorials

Correspondence

Henrietta Varga ([e-mail])