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UniDPlot : A software to detect weak similarities between two DNA sequences

Marc Girondot 1 & Jean-Yves Sire 2

1 Laboratoire d’Écologie, Systématique et Évolution, UMR 8079 Centre National de la Recherche Scientifique, Université Paris Sud et ENGREF, 91405 Orsay cedex 05, France
2 Université Pierre & Marie Curie-Paris 6, UMR 7138 "Systématique, Adaptation, Evolution", 7 quai St-Bernard, 75005 Paris, France

Search for DNA sequence similarity is a crucial step in many evolutionary analyses and several bioinformatic tools are available to fulfill this task. Basic Local Alignment Search Tool (BLAST) is the most commonly and highly efficient algorithm used. However, it often fails in identifying sequences showing very weak similarity. An alternative method is to use Dot Plot, but such a graphical method is not suitable for the analysis of large sequences (e.g. hundreds of kilobases) as this is now more often required in the context of genome sequencing programs.
As an alternative to the classical Dot Plot method, we designed UniDPlot, which permits to search for weak similarity either between two large sequences (e.g., genome regions, ...) or between one large sequence and a short one (e.g., exons, ...).

Current version 1.2.2

Windows version
http://www.bioinformatics.org/unidplot/software/UniDPlot_Win.zip

MacOS version - Universal binaries
http://www.bioinformatics.org/unidplot/software/UniDPlot_Mac.zip