Graphical Representation Of DNA Research Articles

Canonical labels for protein spots of proteomics maps

We consider the problem of canonical labeling for a class of maps, which include proteomics maps, which consist of a set of vertices or protein spots. If this problem is solved and followed, different laboratories studying proteomics maps will arrive at the same numbering of spots, which would facilitate comparisons of data from different sources. In addition, the proposed canonical numberings of protein spots would allow compiling a catalog of proteomics maps just as canonical labeling allows making catalogs graphs, or molecules, and other canonically labeled systems, which would make search for similar sets of maps very efficient. We approach the problem by modifying the algorithm of Jeffrey for graphical representation of DNA based on the chaos game. Graphical representation of DNA as a chaos game map has an important property in that this representation allows one to assign sequential labels to spots in a DNA map. We have modified the approach for sequential labeling of chaos game map representations to graphical representation of any tabular data, such as listing of (x, y) coordinates of protein spots of proteomics maps.

Spectrum‐like graphical representation of RNA secondary structure

AbstractWe consider graphical representation for RNA secondary structure by assigning four horizontal lines to the unpaired bases A, C, G, U and four horizontal lines to paired bases A′, C′, G′, U′. The RNA graphical representation based on eight equidistant horizontal lines can be viewed as natural extension of the earlier four‐line graphical representation of DNA (Randić et al., Chem Phys Lett, 2003, 371, 202) to RNA. Numerical characterization of RNA is based on 8 × 8 matrices recording the adjacency of the nucleotide bases in the primary sequence of RNA when RNA is read from 5′ to 3′. The approach is illustrated on a set of nine viral RNAs, reported in the literature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

A 2-D graphical representation of protein sequences based on nucleotide triplet codons

Graphical representation of DNA provides a simple way of viewing, sorting and comparing various gene structures. A 2-D graphical representation of protein sequences based on nucleotide triplet codons has been derived for similarity analysis of protein sequences. This approach is based on a graphical representation of triplets of DNA in which the interior of the left half plane of the complex plane is used to accommodate 64 sites for the 64 codons. We associate a directed curve, numerical value, or matrix with a protein as a descriptor. The approach is illustrated on the Homo sapiens X-linked nuclear protein (ATRX) gene.

Four-color map representation of DNA or RNA sequences and their numerical characterization

We put forward a novel 2-D graphical representation of DNA or RNA sequences based on a four-color map. The novel representation is rather compact and it not only enables one to carry out a visual inspection of similarity/dissimilarity between DNA sequences, but also leads to their numerical characterization. The approach is illustrated with the coding sequence of the exon 1 of the human β-globin gene.

Unique graphical representation of protein sequences based on nucleotide triplet codons

We consider a graphical representation of proteins as an alternative to the usual representation of proteins as a sequence listing the natural amino acids. The approach is based on a graphical representation of triplets of DNA in which the interior of a square or the interior of a tetrahedron is used to accommodate 64 sites for the 64 codons. By associating a zigzag curve and various matrices with a protein, just as was the case with graphical representation of DNA, one can construct selected invariants to serve as protein descriptors. The approach is illustrated on the A-chain of human insulin.

On a 3-D representation of DNA primary sequences.

We introduce a graphical representation of DNA primary sequences by taking four special vectors in a 3-D space to represent the four nucleic acid bases in DNA sequences, so that a DNA primary sequence is denoted in a 3-D space by a successive vector sequence which is a directed walk on the space. It is demonstrated that this representation has no overlap and intersection and allows numerical characterization.