GBKviz: Genbank Data Visualization WebApp

Table of contents

• Overview
• Install
• Command Usage
• Genome Comparison

Overview

GBKviz is a web-based Genbank data visualization and comparison tool developed with streamlit web framework. GBKviz allows user to easily and flexibly draw CDSs in user-specified genomic region (PNG or SVG format is available). It also supports drawing genome comparison results by MUMmer. This software is developed under the strong inspiration of EasyFig.

Click here to try GBKviz on Streamlit Cloud.

:warning: Due to the limited resources in Streamlit Cloud, it may be unstable.

Install

GBKviz is implemented in Python3 (Tested on Ubuntu20.04)

Install PyPI stable version with pip:

pip install gbkviz

If you want to enable genome comparison in GBKviz, MUMmer is required.

Install MUMmer with apt command (Ubuntu):

sudo apt install mummer

Dependencies

• Streamlit
  Simple web framework for data analysis

• BioPython
  Utility tools for computational molecular biology

• MUMmer
  Genome alignment tool for comparative genomics

Command Usage

Launch GBKviz in web browser (http://localhost:8501):

gbkviz_webapp

Genome Comparison

In GBKviz, MUMmer is used as genome comparison tool.
Following four genome comparison methods are available.

• Nucleotide One-to-One Mapping
• Nucleotide Many-to-Many Mapping
• Protein One-to-One Mapping
• Protein Many-to-Many Mapping

User can download and check genome comparison results file.
Genome comparison results file is in the following tsv format.