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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

The CGView Server: a comparative genomics tool for circular genomes.

Jason R Grant¹, Paul Stothard

¹Department of Agricultural, Food and Nutritional Science, University of Alberta, Canada.

Nucleic Acids Research

|April 16, 2008

Summary

This summary is machine-generated.

The CGView Server creates visual maps of circular genomes, displaying sequence features and analysis results. This tool aids in comparing genomes and identifying genetic variations.

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Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Visualizing genomic data is crucial for understanding genome structure and function.
Existing tools may lack comprehensive features for circular genome mapping and comparative analysis.

Purpose of the Study:

To present the CGView Server, a web-based tool for generating graphical maps of circular genomes.
To provide a user-friendly platform for visualizing sequence features, comparative genomics, and analysis results.

Main Methods:

The CGView Server accepts sequences in various formats (raw, FASTA, GenBank, EMBL) and GFF files for feature annotation.
It utilizes BLAST for sequence similarity searches against up to three comparison genomes.
Graphical maps are generated, offering both overview and detailed regional views of genomic data.

Main Results:

The server produces customizable graphical maps of circular genomes, including bacterial, plasmid, chloroplast, and mitochondrial DNA.
It visualizes sequence features, base composition, analysis outcomes, and sequence similarity plots.
The tool effectively aids in identifying conserved segments, horizontal gene transfer, and gene copy number variations.

Conclusions:

The CGView Server is a valuable resource for visualizing and analyzing circular genomes.
It facilitates comparative genomics and the exploration of genomic diversity.
The server supports diverse applications in microbial genomics and evolutionary studies.