DNA WALKS IN VIRUS GENOMICS

Journal of Chemical Information and Modeling, 2002

Some 2-D and 3-D graphical representations of DNA sequences have been given by Nandy, Leong and Mogenthaler, and Randic et al., which give visual characterizations of DNA sequences. In this paper, we presented a novel graphical representation of DNA sequences by taking four special vectors in 2-D Cartesian coordinate system to represent the four nucleic acid bases in DNA sequences, so that a DNA sequence is denoted on a plane by a directed walk. It is shown that the new graphical representation of DNA sequences has lower or nondegeneracy.

Physical Review E, 2003

DNA sequences are represented as two-dimensional walkers based on groups of mapping rules for the nucleotides in the DNA sequences. Digital sequences from irrational and random numbers in base 4 are generated and their diffusion properties are then compared with those of 21 nucleotide sequences of animal and plant viruses. By defining the diffusion coefficient as a function of the number of steps taken in a walk, we show that the coefficients for the viral DNA sequences generally have maximum values considerably larger than those for the random-number sequences of same lengths. Moreover, using the walker diagrams generated by different mapping groups, we can study the dominance of any of the nucleotide pairs ͑AG or CT͒, ͑AC or GT͒, or ͑AT or CG͒ in a DNA sequence. Other possible studies of this approach are mentioned.

Proceedings of the 6th International Conference on Information Visualization Theory and Applications, 2015

This article describes a three-channel encoding of nucleotide sequences, and proper formulas for filtering and downsampling such encoded sequences for multi-scale signal analysis. With proper interpolation, the encoded sequences can be visualized as curves in three-dimensional space. The filtering uses Gaussian-like smoothing kernels, chosen so that all levels of the multi-scale pyramid (except the original curve) are practically free from aliasing artifacts and have the same degree of smoothing. With these precautions, the overall shape of the space curve is robust under small changes in the DNA sequence, such as single-point mutations, insertions, deletions, and shifts.

Chemical Physics Letters, 2003

We consider a novel 2-D graphical representation of DNA sequences preserving information on sequential adjacency of bases and allowing numerical characterization. The representation avoids loss of information accompanying alternative 2-D representations in which the curve standing for DNA overlaps and intersects itself. The method is illustrated on the coding sequence of the first exon of human b-globin gene.

Chemical Physics Letters, 2007

A new 'dynamic' 2D-graphical representation of DNA sequences is presented. The model is based on 2D-plots that have been used before and are easy to visualize, but it removes many degeneracies present in the previous approaches. The moments of inertia of the 'dynamic' graphs are proposed as a new kind of descriptor for DNA sequences.

Journal of Biosciences, 1998

The advent of automated DNA sequencing techniques has led to an explosive growth in the number and length of DNAs sequenced frpm different organisms. While this has resulted in a large accumulation of data in the DNA databases, it has also called for the development of suitable techniques for rapid viewing and analysis of the data. Over the last few years several methods have been proposed that address these issues and represent a DNA sequence in a compact graphical form in one-, two-or three-dimensions that can be expanded as necessary to help visualize the patterns in gene sequences and aid in in-depth analysis. Graphical techniques have been found to be useful in highlighting local and global base dominances, to identify regions of extensive repetitive sequences, differentiate between coding and non-coding regions, and to be indicative of evolutionary divergences. Analysis with graphical methods have also provided insights into new structures' in DNA sequences such as fractals and long range correlations, and some measures have been developed that help quantify the visual patterns.

Chemical Physics Letters, 2001

Some 2-D and 3-D graphical representations of DNA sequences have been given by Nandy, Leong and Mogenthaler, and Randic et al., which give visual characterizations of DNA sequences. In this Letter, we introduce a novel graphical representation of DNA sequences by taking four special vectors in 2-D space to represent the four nucleic acid bases in DNA sequences, so that

Journal of Molecular Modeling, 2014

A new 3D graphical representation of DNA sequences is introduced. This representation is called 3Ddynamic representation. It is a generalization of the 2Ddynamic dynamic representation. The sequences are represented by sets of "material points" in the 3D space. The resulting 3D-dynamic graphs are treated as rigid bodies. The descriptors characterizing the graphs are analogous to the ones used in the classical dynamics. The classification diagrams derived from this representation are presented and discussed. Due to the third dimension, "the history of the graph" can be recognized graphically because the 3D-dynamic graph does not overlap with itself. Specific parts of the graphs correspond to specific parts of the sequence. This feature is essential for graphical comparisons of the sequences. Numerically, both 2D and 3D approaches are of high quality. In particular, a difference in a single base between two sequences can be identified and correctly described (one can identify which base) by both 2D and 3D methods.

Chemical Physics Letters, 2003

The large number of bases in a DNA sequence and the cryptic nature of the 4-alphabet representation make graphical visualization of DNA sequences useful for biologists. However, existing 3D graphical representations are complicated, whereas existing 2D graphical representations suffer from high degeneracy, and many features in a DNA sequence cannot be visualized clearly. This Letter introduces a novel 2D method of DNA representation: the DB-Curve (Dual-Base Curve), which overcomes some of the limitations in existing 2D graphical representations. Many properties of DNA sequences can be observed and visualized easily using a combination of DB-Curves. The new representation can avoid degeneracy completely compared to existing 2D graphical representations of DNA sequences. Unlike 3D graphical representations, no 2D projection is required for the DB-Curve, and this allows for easier analysis of DNA sequences. The DB-Curve provides a useful graphical tool for the visualization and study of DNA sequences.

Biochimie, 1985

R~sum~ --Si dans l'~criture d'une sdquence d'acide nucldique on remplace les quatre lettres C, G, A, T (ou U) par des symboles graphiques approprids, on peut faire apparaftre irnmddiatement certains motifs. Des jeux de symboles, construits soit pour l'analyse des alternances purinepyrimidine, soit pour celle des compldmentaritds clans une sdquence sont pr~sentds. Par ailleurs, en faisant correspondre aux quatre nuclgotides quatre vecteurs dans le plan, on transforme la sdquence en une trajectoire. Nous montrons comment, dans le cas du gdne de l'hdmoglobine humahle bdta, un tel codage permet de discriminer aisdment les introns des exons.