Abstract
We have constructed graphical (qualitative and visual) representations of DNA sequences as 2D maps and their numerical (quantitative and computational) analysis. The maps are obtained by transforming the four-letter sequences (where letters represent the four nucleic bases) via a spiral representation over triangular and square cells grids into a four- color map. The so constructed maps are then represented by distance matrices. We consider the use of several matrix invariants as DNA descriptors for determining the degree of similarity of a selection of DNA sequences.
Highlights
Graphical representations of DNA were initiated by Hamori and Ruskin[1−3] over 25 years ago as an alternative viewing of DNA sequences
Graphical representations allow one to visually estimate the degree of similarity or the lack of similarities among lengthy DNA sequences composed of four bases represented by letters A, C, G and T
Jeffrey modified the algorithm of the Chaos Game to suit representations of DNA sequences and arrived at geometrical patterns that made of large number of points scattered inside a square, which can be viewed as DNA maps
Summary
Graphical representations of DNA were initiated by Hamori and Ruskin[1−3] over 25 years ago as an alternative viewing of DNA sequences. The approach is based on using related geometrical templates in construction of alternative maps for graphical representation of the same set of DNA sequences.
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