Representation Of DNA Sequences Research Articles

H– L curve: A novel 2D graphical representation for DNA sequences

By assigning to four kinds of basic nucleotide A, T, G and C, respectively, four different two-component vectors, in which the first elements are constant (equal to 1) and the second elements are different from each other, we presented a 2D graphical representation of DNA primary sequences, which is mathematically proven to be not any circuit and associated with DNA sequences in a one-to-one manner and whose advantage is that it helps in identifying major difference among similar DNA sequences. Making use of the presented graphical representation, we analyzed DNA mutations between sequences.

Analysis of similarity/dissimilarity of DNA sequences based on a class of 2D graphical representation

On the basis of a class of 2D graphical representations of DNA sequences, sensitivity analysis has been performed, showing the high-capability of the proposed representations to take into account small modifications of the DNA sequences. And sensitivity analysis also indicates that the absolute differences of the leading eigenvalues of the L/L matrices associated with DNA increase with the increase of the number of the base mutations. Besides, we conclude that the similarity analysis method based on the correlation angles can better eliminate the effects of the lengths of DNA sequences if compared with the method using the Euclidean distances. As application, the examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species has been performed by our method, and the reasonable results verify the validity of our method.

Another look at the chaos-game representation of DNA

Abstract We have considered the chaos game representation of short DNA sequences (about 100 bases instead of 100 000 bases considered by Jeffrey and others) and have outlined a procedure which converts the corresponding 2D DNA maps into ‘spectrum-like’ format, which offer not only a better visual representations but also makes possible a visual inspection of the degree of similarity among different DNA sequences.

Simulation for chaos game representation of genomes by recurrent iterated function systems

Chaos game representation (CGR) of DNA sequences and linked protein sequences from genomes was proposed by Jeffrey (1990) and Yu et al. (2004), respectively. In this paper, we consider the CGR of three kinds of sequences from complete genomes: whole genome DNA sequences, linked coding DNA sequences and linked protein sequences. Some fractal patterns are found in these CGRs. A recurrent iterated function systems (RIFS) model is proposed to simulate the CGRs of these sequences from genomes and their induced measures. Numerical results on 50 genomes show that the RIFS model can simulate very well the CGRs and their induced measures. The parameters estimated in the RIFS model reflect information on species classification.

A group of 3D graphical representation of DNA sequences based on dual nucleotides

AbstractBased on chemical properties of the neighboring dual nucleotides, we reduce a DNA sequence into four 3D graphical representations. Associating with the eigenvalues of the introduced covariance matrix and the introduced measure of similarity, we introduce an approach to make similarity analysis of DNA sequence. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Evidence for recombination between PCV2a and PCV2b in the field

Genomic sequence analysis demonstrates that porcine circovirus type 2 (PCV2) isolates are divided into distinct genotypes. Historically, swine herds in the U.S. have been infected with the PCV2a genotype. In 2005, PCV2b was identified in North America and with it increased reports of porcine circovirus disease (PCVD). A differential PCR technique incorporating PCV2 genotype-specific primers was used in the clinical diagnosis of PCVD. A set of 97 diagnostic submissions showed that both PCV2a and PCV2b were present in 25% of clinical samples. The construction of phylogenetic trees using whole genome sequences from diagnostic submissions showed that one isolate, 0737A, was only loosely associated with other PCV2b isolates. Analysis of the variable sites between representative PCV2a and PCV2b DNA sequences and the 0737A sequence, showed that 0737A was a mosaic sequence, with the ORF1 region from PCV2a and ORF2 from PCV2b. This study demonstrates that pigs can be naturally infected with multiple PCV2 genotypes and that PCV2a/PCV2b recombination events occur in the field.

Visualization of DNA sequences based on 3DD-Curves

In this paper we (1) introduce a new 3D graphical representation of DNA sequences; (2) visualize DNA sequences based on 3DD-Curves; (3) provide a new invariant of DNA sequences based on our 3DD-Curve. All this represents a new development of graphical representation and numerical characterization for DNA sequences.

New 3D graphical representation of DNA sequence based on dual nucleotides

We introduce a 3D graphical representation of DNA sequences based on the pairs of dual nucleotides (DNs). Based on this representation, we consider some mathematical invariants and construct two 16-component vectors associated with these invariants. The vectors are used to characterize and compare the complete coding sequence part of beta globin gene of nine different species. The examination of similarities/dissimilarities illustrates the utility of the approach.

ANALYSIS OF SIMILARITY/DISSIMILARITY OF DNA SEQUENCES BY A NEW 3D GRAPHICAL REPRESENTATION

A new 3D graphical representation of DNA sequences according to chemical structures of the bases is proposed, reflecting the distribution of bases with different chemical structure, preserving information on sequential adjacency of bases, avoiding loss of information accompanying alternative 3D representations in which the curve standing for DNA overlaps and intersects itself. Based on this representation, a numerical characterization approach is presented by constructing a six-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with the DNA sequences. The examination of similarities among the coding sequences of the first exon of β-globin gene of different species illustrates the utility of the approach.

On property of the invariant of graphical representations of DNA sequences

In this article, we consider the influence of variation of DNA sequence on the leading eigenvalue of graphical representation of the biological sequences. The research interpret the rationality of the graphical representation method that compare different DNA sequences. And we show the result on two different models that presented before.

PN-curve: A 3D graphical representation of DNA sequences and their numerical characterization

We consider a novel 3D graphical representation of DNA sequences based on the pairs of nucleotides (PNs). The model avoids loss of information accompanying alternative 3D representations in which the curve standing for DNA sequence overlaps or intersects itself. The utility of the method can be illustrated by the examination of similarities/dissimilarities among the complete coding sequence part of beta globin gene of several different species.

2D-dynamic representation of DNA sequences

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.

Novel 2D graphical representation of DNA sequence based on dual nucleotides

Based on the neighboring dual nucleotides, we introduce a novel 2D graphical representation of DNA sequences. We associate each sequence with mutation properties of neighboring bases by giving a 2D graphical representation, and thus obtain a seven-component vector relative to seven different classifications of mutations. The introduced vector is applied to characterize and compare the coding sequences of the first exon of β-globin gene of 11 different species.

Analysis of Similarity/Dissimilarity of Long DNA Sequences Based on Three 2DD-Curves

Some 2D graphical representations of DNA sequences have been reported by several authors, which give visual characterizations of DNA sequences. In this paper, we present a new 2D graphical representation of DNA sequences without degeneracy. Furthermore, we propose two methods for the visualization and analysis of long DNA sequences.

Novel numerical and graphical representation of DNA sequences and proteins

We have introduced novel numerical and graphical representations of DNA, which offer a simple and unique characterization of DNA sequences. The numerical representation of a DNA sequence is given as a sequence of real numbers derived from a unique graphical representation of the standard genetic code. There is no loss of information on the primary structure of a DNA sequence associated with this numerical representation. The novel representations are illustrated with the coding sequences of the first exon of β-globin gene of half a dozen species in addition to human. The method can be extended to proteins as is exemplified by humanin, a 24-aa peptide that has recently been identified as a specific inhibitor of neuronal cell death induced by familial Alzheimer's disease mutant genes.

A novel unexpected use of a graphical representation of DNA: Graphical alignment of DNA sequences

We outline an unexpected use of a particular graphical representation of DNA sequences, the ‘four line’ graphical representation [M. Randić, M. Vračko, N. Lerš, D. Plavšić, Chem. Phys. Lett. 368 (2003) 1] and how it can facilitate solving problem of DNA sequence alignment. The approach is exemplified by two shorter DNA sequences.

PNN-curve: A new 2D graphical representation of DNA sequences and its application

We introduce a novel 2D graphical representation of DNA sequences based on the pairs of the neighboring nucleotides (PNNs). Then we get the PNNs’ distributions and obtain a y-M. The construction of the PNN-curve has some important advantages ( 1 ) It avoids loss of information and the PNN-curve standing for DNA sequences does not overlap or intersect with itself. (2) The novel 2D representation is more sensitive. The utility of this method can be illustrated by the examination of similarities/dissimilarities among the coding sequences of the first exon of β -globin gene of eleven different species in Table 2.

A representation of DNA primary sequences by random walk

We describe the DNA primary sequences by random walk. With the description, two random sequences {Ym} and {Xn} corresponding to a DNA sequence, as well as graphical representations of DNA sequences are given. We further prove that two random sequences {Ym} and {Xn} are both Markov chains. Based on transition probability distributions of Markov chains, some numerical characterizations of random sequences, we introduce some new invariants for the DNA primary sequences. Then using these invariants, we make comparisons among primary sequences for exon 1 of β-globin genes belonging to nine species for analysis of the similarity and dissimilarity.

Coronavirus phylogeny based on 2D graphical representation of DNA sequence.

A novel coronavirus has been identified as the cause of the outbreak of severe acute respiratory syndrome (SARS). Previous phylogenetic analyses based on sequence alignments show that SARS‐CoVs form a new group distantly related to the other three groups of previously characterized coronaviruses. In this aritcle, a new approach based on the 2D graphical representation of the whole genome sequence is proposed to analyze the phylogenetic relationships of coronaviruses. The evolutionary distances are obtained through measuring the differences among the two‐dimensional curves. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1196–1202, 2006

On the Similarity of DNA Primary Sequences Based on 5-D Representation

We propose a 5-D representation of DNA sequences based on the classifications of the four basic acid bases A,T,G, and C. The use of the 5-D representation is illustrated by constructing sequence invariants based on the entries in derived sequence matrices restricted to a selected width of a band along the main diagonal. As an application, we make a comparison for the first exon of β-globin gene sequences belonging to eleven different species based on the 5-D representation.