GraphDNA: a Java program for graphical display of DNA composition analyses

GraphDNA: a Java program for graphical display of DNA composition analyses

Tcherepanov Vasily, Brown Gordon, Horspool Daniel, Thomas Jamie M, Upton Chris

Abstract Background Under 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. Results 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. Conclusion GraphDNA 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.

2007

DOI: 10.1186/1471-2105-8-21

BMC Bioinformatics

BMC

Biology (General), Computer applications to medicine. Medical informatics

EN