Novel techniques of graphical representation and analysis of DNA sequences—A review

Roy, A. K.; Raychaudhury, Chandan; Nandy, Ashesh

doi:10.1007/bf02728525

Cited by 85 publications

(52 citation statements)

References 42 publications

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“…In recent years many different graphical representations of DNA/protein sequences have been reported (Gates, 1986;Roy et al, 1998;Li et al, 2006;Randiü et al, 2007;González-Díaza et al, 2009; and the references therein).…”

Section: Introductionmentioning

confidence: 99%

Similarity analysis for DNA sequences based on chaos game representation. Case study: The albumin

Stan

Cristescu

Scarlat

2010

Journal of Theoretical Biology

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Section: Introductionmentioning

confidence: 99%

Similarity analysis for DNA sequences based on chaos game representation. Case study: The albumin

Stan

Cristescu

Scarlat

2010

Journal of Theoretical Biology

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“…Here again is branching, and we move to vertex 14 (having the smaller label) and end with vertex 19. In this way, we passed above the additional five edges: (5, 6); (6, 7); (7,8); (8,14); and (14,19), adding five more zeros to our code, the beginning of which is now 0 0 0 0 0 0 0 0 0. The vertex 19 is the end of travel so far, and we have to go back toward vertex 14 and 8.…”

Section: Review Wwwq-chemorgmentioning

confidence: 99%

“…The vertex 19 is the end of travel so far, and we have to go back toward vertex 14 and 8. We assign to edges (19,14) and (14,8) labels 1, because we passed these edges before. This continues the code: 0 0 0 0 0 0 0 0 0 1 1.…”

Section: Review Wwwq-chemorgmentioning

confidence: 99%

“…[6,7,35,36] For early developments of graphical bioinformatics, see the review article by A. Roy, C. Raychaudhury, and A. Nandy. [8] In the year 2000, graphical bioinformatics saw an important novelty that resulted in the expansion from this so-far essentially qualitative graphical bioinformatics, a visual discipline, into a quantitative discipline of graphical bioinformatics, defined by the numerical characterization of DNA. [9,37,38] Soon followed extensions of this numerical characterization to RNA and the introduction of the first graphical representations of proteins accompanied by the numerical characterization of proteins.…”

Section: Introductionmentioning

confidence: 99%

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Milestones in graphical bioinformatics

Randić

Novič

Plavšić

2013

Int J of Quantum Chemistry

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After reviewing the field of graphical bioinformatics, we have selected two dozen of the most significant publications that represent milestones of graphical bioinformatics. These publications can be viewed as forming the backbone of graphical bioinformatics, the branch of bioinformatics that initiates analysis of DNA, RNA, and proteins by considering various graphical representations of these sequences. Graphical bioinformatics, a division of bioinformatics that analyzes sequences of DNA, RNA, proteins, and proteomics maps by developing and using tools of discrete mathematics and graph theory in particular, has expanded since the year 2000, although pioneering contributions date back to Hamory (1983) and Jeffrey (1990). We chronologically follow the development of graphical bioinformatics, without assuming that readers are familiar with discrete mathematics or graph theory. Readers unfamiliar with graph theory may even have some advantage over those who have been only superficially exposed to graph theory, inview of wide misconceptions and misinformation about chemical graph theory among quantum chemists, physical chemists, and medicinal chemists in past decades. © 2013 Wiley Periodicals, Inc.

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“…As far as the application of molecular systematics in chemistry or biochemistry is concerned, considerable efforts have been made to develop visual and computational methods for studying individual gene or protein sequences, their structures, functions, repetitive sequences, and nucleotide or amino acid frequencies (Roy et al, 1998). For studying structural relationships in individual macromolecules, the most preferred algorithms are based on graph-theoretical methods.…”

Section: Introductionmentioning

confidence: 99%

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

Jakó¹,

Ari²,

Ittzés³

et al. 2009

Molecular Phylogenetics and Evolution

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Novel techniques of graphical representation and analysis of DNA sequences—A review

Cited by 85 publications

References 42 publications

Similarity analysis for DNA sequences based on chaos game representation. Case study: The albumin

Similarity analysis for DNA sequences based on chaos game representation. Case study: The albumin

Milestones in graphical bioinformatics

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

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