Graphical Representation Of DNA Sequences Research Articles

Application of 2-D graphical representation of DNA sequence

Recently, we proposed a 2-D graphical representation of DNA sequence [Bo Liao, A 2-D graphical representation of DNA sequence, Chem. Phys. Lett. 401 (2005) 196–199]. Based on this representation, we consider properties of mutations and compute the similarities among 11 mitochondrial sequences belonging to different species. The elements of the similarity matrix are used to construct phylogenic tree. Unlike most existing phylogeny construction methods, the proposed method does not require multiple alignment.

Graphical approach to analyzing DNA sequences

Recently, we proposed a 2D graphical representation of DNA sequence [J Comput Chem 25(2004) 1364-1368]. Based on this representation, we outline one approach to search optimal alignment. We also can judge the mutations between bases and an unknown sequence based on its graph and a known sequence's graph.

On 2D graphical representation of DNA sequence of nondegeneracy

Some two-dimensional (2D) graphical representations of DNA sequences have been given by Gates, Nandy, Leong and Mogenthaler, Randić, and Liao et al., which give visual characterizations of DNA sequences. In this Letter, we introduce a nondegeneracy 2D graphical representation of DNA sequence, which is different from Randić’s novel 2D representation and Liao’s 2D representation. We also present the nondegeneracy forms corresponding to the representations of Gates, Nandy, Leong and Mogenthaler.

A new 2-D graphical representation of DNA sequences and their numerical characterization

We consider a novel 2-D graphical representation of DNA sequences according to chemical structures of bases, reflecting distribution of bases with different chemical structure, 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. Based on this representation we present a numerical characterization approach by the leading eigenvalues of the matrices associated with the DNA sequences. The utility of the approach is illustrated on the coding sequences of the first exon of human β-globin gene.

Analysis of similarity/dissimilarity of DNA sequences based on a condensed curve representation

Recently we proposed a 3D graphical representation of DNA sequences [B. Liao, T. Wang, 3-D graphical representation of DNA sequences and their numerical characterization, Journal of Molecular Structure: THEOCHEM 681 (2004) 209–212]. Based on this representation, we outline one such approach by constructing a 3-component vector whose components are the leading eigenvalues of the L/ L matrices associated with DNA sequences. The examination of similarities/dissimilarities among the coding sequences of the first exon of β-globin gene of different species illustrates the utility of the approach.

A 2D graphical representation of DNA sequence

A 2D graphical representation of DNA sequences using a two-quadrant cartesian coordinates system has been derived for mathematical denotation of DNA sequence. The 2D graphical representation also avoids loss of information accompanying alternative 2D and 3D representation in which the curve standing for DNA sequence overlaps and intersects itself, and resolves sequences’ degeneracy. The geometrical centers of the two dimension graph of DNA sequences indicate the distribution of base frequencies with different parameter n and m.

A class of new 2-D graphical representation of DNA sequences and their application

We propose the concepts of cell and system of graphical representation of DNA sequences, and introduce a class of 2-D graphical representations based on different designed cells. The representation also avoids loss of information associated with crossing and overlapping of the corresponding curve. As application, we outline one such approach, which is based on the construction of a vector whose components are the normalized leading eigenvalues of the L/ L matrices associated with DNA. The examination of similarities/dissimilarities among the coding sequences of the first exon of β-globin gene of different species illustrates the utility of the approach.

3-D graphical representation of DNA sequences and their numerical characterization

We introduce a 3-D graphical representation of DNA sequences, L-curve. L-curve also avoids loss of information accompanying alternative 2-D and 3-D representation 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 β-globin gene.

Highly compact 2D graphical representation of DNA sequences

Most 2D graphical representations of primary DNA sequences, while offering visual geometrical patterns for depicting sequences, do require considerable space if enough details of such representations are to be visible. In this contribution, we consider a highly compact graphical representation of DNA, which allows visual inspection and numerical characterization of DNA sequences having a large number of nucleic acid bases. The approach is illustrated on the DNA sequences of the first exon of human β-globin. The same graphical approach not only allows one to depict differences in composition within a single DNA, but makes possible graphical representation of protein sequences, which have hitherto evaded similar 2D visual representations.

New 2D graphical representation of DNA sequences.

We consider a 2D graphical representations of DNA sequences, which avoids loss of information associated with crossing and overlapping of the corresponding curve. We outline an approach, which is based on the construction of a three-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with DNA. The examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species illustrates the utility of the approach.

Analysis of similarity/dissimilarity of DNA sequences based on 3-D graphical representation

Recently, we proposed a 3-D graphical representation of DNA sequences [Chem. Phys. Lett. 379 (2003) 412]. Based on this representation, we outline one such approach by constructing a 15-component vector whose components are the average bandwidth of the D/ D matrices. The examination of similarities/dissimilarities among the coding sequences of the first exon of β-globin gene of different species illustrates the utility of the approach.

New 3D graphical representation of DNA sequences and their numerical characterization

We consider a 3D graphical representation of DNA sequences and their numerical characterization. The representation also avoids loss of information accompanying alternative 2D and 3D representation 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 β-globin gene.

DNA sequence representation without degeneracy

Graphical representation of DNA sequence provides a simple way of viewing, sorting and comparing various gene structures. A new two-dimensional graphical representation method using a two- quadrant Cartesian coordinates system has been derived for mathematical denotation of DNA sequence. The two-dimensional graphic representation resolves sequences' degeneracy and is mathematically proven to eliminate circuit formation. Given x-projection and y-projection of any point on the graphical representation, the number of A, G, C and T from the beginning of the sequence to that point could be found. Compared with previous methods, this graphical representation is more in-line with the conventional recognition of linear sequences by molecular biologists, and also provides a metaphor in two dimensions for local and global DNA sequence comparison.

Compact 2-D graphical representation of DNA

We present a novel 2-D graphical representation for DNA sequences which has an important advantage over the existing graphical representations of DNA in being very compact. It is based on: (1) use of binary labels for the four nucleic acid bases, and (2) use of the ‘worm’ curve as template on which binary codes are placed. The approach is illustrated on DNA sequences of the first exon of human β-globin and gorilla β-globin.

Numerical characterization of DNA sequences in a 2-D graphical representation scheme of low degeneracy

Some 2-D and 3-D graphical representations of DNA sequences have been given by Gate, Nandy, Leong, Randic, and Guo et al. Based on 2-D graphical representation of DNA sequences, Raychaudhury and Nandy introduced the first-order moments of the x and y coordinates and the radius of the plot of a DNA sequence for indexing scheme and similarity measures of DNA sequences. In this Letter, based on Guo’s novel 2-D graphical representation of DNA sequences of low degeneracy, we introduce the improved first-order moments of the x and y coordinates and the radius of DNA sequences, and the distance of two DNA sequences. The new descriptors of DNA sequences give a good numerical characterization of DNA sequences, which have lower degeneracy.

Novel 2-D graphical representation of DNA sequences and their numerical characterization

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 β-globin gene.

DB-Curve: a novel 2D method of DNA sequence visualization and representation

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.

ChemInform Abstract: Some Notes on 2‐D Graphical Representation of DNA Sequence.

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Some notes on 2-D graphical representation of DNA sequence.

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.

A novel 2-D graphical representation of DNA sequences of low degeneracy

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 a DNA sequence is denoted on a plane by a successive vector sequence, which is also a directed walk on the plane. It is showed that the novel graphical representation of DNA sequences has lower degeneracy and less overlapping.