isDNA: A Tool for Real-Time Visualization of Plasmid DNA Monte-Carlo Simulations in 3D

Computational simulation of plasmid DNA (pDNA) molecules, owning a closed-circular shape, has been a subject of study for many years. Monte-Carlo methods are the most popular family of methods that have been used in pDNA simulations. However, though there are many software tools for assembling and v...

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Bibliographic Details
Published inBioinformatics and Biomedical Engineering pp. 566 - 577
Main Authors Raposo, Adriano N., Gomes, Abel J. P.
Format Book Chapter
LanguageEnglish
Published Cham Springer International Publishing 2015
SeriesLecture Notes in Computer Science
Subjects
Monte-Carlo
pDNA
simulation
software
visualization
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Summary:Computational simulation of plasmid DNA (pDNA) molecules, owning a closed-circular shape, has been a subject of study for many years. Monte-Carlo methods are the most popular family of methods that have been used in pDNA simulations. However, though there are many software tools for assembling and visualizing DNA molecules, none of them allows the user to visualize the course of the simulation in 3D. As far as we know, we present here the first software (called isDNA) allowing the user to visualize 3D MC simulations of pDNA in real-time. This is sustained on an adaptive DNA assembly algorithm that uses Gaussian molecular surfaces of the nucleotides as building blocks, and an efficient deformation algorithm for pDNA’s MC simulations.
ISBN:9783319164793
3319164791
ISSN:0302-9743
1611-3349
DOI:10.1007/978-3-319-16480-9_54