Work

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

Year: 2022

Type: article

Abstract: The Context-dependent Mutation Analysis Package and Visualization Software (CDMAP/CDVIS) is an automated, modular toolkit used for the analysis and visualization of context-dependent mutation patterns (site-specific variation in mutation rate from neighboring-nucleotide effects). The CDMAP computes context-dependent mutation rates using a Variant Call File (VCF), Genbank file, and reference genome and can generate high-resolution figures to analyze variation in mutation rate across spatiotemporal scales. This algorithm has been benchmarked against mutation accumulation data but can also be used to calculate context-dependent mutation rates for polymorphism or closely related species as long as the input requirements are met. Output from CDMAP can be integrated into CDVIS, an interactive database for visualizing mutation patterns across multiple taxa simultaneously.

Source: G3 Genes Genomes Genetics

DOI: 10.1093/g3journal/jkac299

Authors: David L Patton, Thomas Cardenas, Perrin Mele, Jon Navarro, Way Sung

Institution: University of North Carolina at Charlotte

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,580

Funder: National Science Foundation