Graphical representations of DNA as 2-D map

We describe a modification of the compact representation of DNA sequences which transforms the sequence into a 2-D diagram in which the 'spots' have integer coordinates. As a result the accompanying numerical characterization of DNA is quite simple and straightforward. This is an important advantage, particularly when considering DNA sequences having thousands of nucleic bases. The approach starts with the compact representation of DNA based on zigzag spiral template used for placing 'spots' associated with binary codes of the nucleic acids and subsequent suppression of the underlying zigzag curve. As a result, a 2-D map is formed in which all 'spots' have integer coordinates. By using only distances between spots having the same x or the same y coordinate one can construct a 'map profile' using integer arithmetic. The approach is illustrated on DNA sequences of the first exon of human beta-globin. (C) 2004 Elsevier B.V. All rights reserved.