Abstract
BackgroundUnder conditions of no strand bias the number of Gs is equal to that of Cs for each DNA strand; similarly, the total number of Ts is equal to that of As. However, within each strand there are considerable local deviations from the A = T and G = C equality. These asymmetries in nucleotide composition have been extensively analyzed in prokaryotic and eukaryotic genomes and related to chromosome organization, transcription orientation and other processes in certain organisms. To carry out analysis of intra-strand nucleotide distribution several graphical methods have been developed.ResultsGraphDNA is a new Java application that provides a simple, user-friendly interface for the visualization of DNA nucleotide composition. The program accepts GenBank, EMBL and FASTA files as an input, and it displays multiple DNA nucleotide composition graphs (skews and walks) in a single window to allow direct comparisons between the sequences. We illustrate the use of DNA skews for characterization of poxvirus and coronavirus genomes.ConclusionGraphDNA is a platform-independent, Open Source, tool for the analysis of nucleotide trends in DNA sequences. Multiple sequence formats can be read and multiple sequences may be plotted in a single results window.
Highlights
Under conditions of no strand bias the number of Gs is equal to that of Cs for each DNA strand; the total number of Ts is equal to that of As
This paper describes GraphDNA, a new Java software application, that was developed as a platform-independent application to present DNA skews and walks of multiple sequences in a single graph and assist in the comparative analysis of nucleotide composition asymmetry
The time required by GraphDNA to load DNA sequences and display plots is dependent upon the size and number of sequences as well as the nucleotide window size used for calculating skews and walks
Summary
GraphDNA is a new Java application that provides a simple, user-friendly interface for the visualization of DNA nucleotide composition. The program accepts GenBank, EMBL and FASTA files as an input, and it displays multiple DNA nucleotide composition graphs (skews and walks) in a single window to allow direct comparisons between the sequences. We illustrate the use of DNA skews for characterization of poxvirus and coronavirus genomes
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