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Related Experiment Video

Updated: Aug 6, 2025

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

Published on: August 14, 2018

CDMAP/CDVIS: context-dependent mutation analysis package and visualization software.

David L Patton¹, Thomas Cardenas¹, Perrin Mele¹

¹Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, 28223, USA.

G3 (Bethesda, Md.)

|March 14, 2023

Summary

This summary is machine-generated.

The Context-dependent Mutation Analysis Package and Visualization Software (CDMAP/CDVIS) offers automated analysis of mutation rates influenced by neighboring nucleotides. This toolkit visualizes these patterns across species and spatiotemporal scales.

Keywords:

R software context-dependent mutations interactive visualization tool mutation accumulation software package

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Understanding mutation patterns is crucial for evolutionary and disease studies.
Site-specific mutation rates are influenced by the surrounding nucleotide context.
Existing tools may lack comprehensive analysis and visualization of these context-dependent patterns.

Purpose of the Study:

To introduce an automated, modular toolkit for analyzing and visualizing context-dependent mutation patterns.
To provide a method for calculating mutation rates based on neighboring nucleotide effects.
To enable high-resolution visualization of mutation rate variations across different scales and taxa.

Main Methods:

The Context-dependent Mutation Analysis Package (CDMAP) computes mutation rates using Variant Call Files (VCF), Genbank files, and reference genomes.
CDMAP generates high-resolution figures for spatiotemporal mutation rate analysis.
The Visualization Software (CDVIS) integrates CDMAP output for interactive, multi-taxa visualization.

Main Results:

CDMAP has been benchmarked against mutation accumulation data, demonstrating its accuracy.
The toolkit can calculate context-dependent mutation rates for polymorphism and closely related species.
CDVIS allows for simultaneous visualization of mutation patterns across multiple taxa.

Conclusions:

CDMAP/CDVIS provides a robust and automated solution for analyzing context-dependent mutation patterns.
The toolkit facilitates the study of mutation rate variation across diverse evolutionary contexts.
This integrated approach enhances the understanding of mutation dynamics in genomics.