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

Zhang, Qi; Qi, Xiaoqin

doi:10.1016/j.cplett.2007.03.107

Cited by 51 publications

(34 citation statements)

References 18 publications

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“…[12,16,30] Furthermore, some researches proposed other mathematical descriptors, such as 7-vectors. [14] cumulative distance, [31,32] and so on. These methods were proved to be useful and used to resolve more biological problems besides similarity comparison.…”

Section: Applications Mathematical Descriptors For Similarity Analysismentioning

confidence: 99%

Using Huffman coding method to visualize and analyze DNA sequences

Zhang

2011

J Comput Chem

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On the basis of the Huffman coding method, we propose a new graphical representation of DNA sequence. The representation can avoid degeneracy and loss of information in the transfer of data from a DNA sequence to its graphical representation. Then a multicomponent vector from the representation is introduced to characterize quantitatively DNA sequences. The components of the vector are derived from the graphical representation of DNA primary sequence. The examination of similarities and dissimilarities among the complete coding sequences of β-globin gene of 11 species and six ND6 proteins shows the utility of the scheme.

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Section: Applications Mathematical Descriptors For Similarity Analysismentioning

confidence: 99%

Using Huffman coding method to visualize and analyze DNA sequences

Zhang

2011

J Comput Chem

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“…In previous study, most of graphical techniques of DNA sequences are based on the single nucleotide: A, C, G, T. However, there were several researchers who introduced some graphical representations of DNA primary sequences based on the pairs of the neighboring nucleotides such as Liu et al [28], Qi and Qi [39], and Liu et al [38]. In this section, by analyzing and comparing our method with above methods, we will show that our method is superior to others.…”

Section: Comparison With Other Methodsmentioning

confidence: 99%

“…But the dinucleotide content was of equal or greater importance than the single one and DNA structural configurations appeared to be determined principally by base-step arrangements [37]. Therefore, if the theory and method is based on the dinucleotide, much more biological information carried by a DNA sequence could be obtained [28,38,39].…”

Section: Introductionmentioning

confidence: 99%

New graphical representation of a DNA sequence based on the ordered dinucleotides and its application to sequence analysis

Huang

Wang

2011

Int J of Quantum Chemistry

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Graphical representation of a DNA sequence is a powerful tool for basic biological research. Based on the ordered dinucleotides, we propose a novel three dimensional (3D) graphical representation without circuit or degeneracy. Simultaneously, we derive the projection curve of the 3D graph. These two curves have good visualization for longer DNA sequences. The utility of the proposed curves is illustrated by mutation analysis, similarity analysis, and evolutionary relationships of different species. The results indicate that our method is efficient and powerful.

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“…The approaches of this kind (including the variations with some modifications) are utilized in Refs. [8,11,13,14,17,22].…”

Section: Bioinformatics In the Era Of Post Genomics And Big Datamentioning

confidence: 99%

Graphical Representation of Biological Sequences

Mizuta¹

2018

Bioinformatics in the Era of Post Genomics and Big Data

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Sequence comparison is one of the most fundamental tasks in bioinformatics. For biological sequence comparison, alignment is the most profitable method when the sequence lengths are not so large. However, as the time complexity of the alignment is the square order of the sequence length, the alignment requires a large amount of computational time for comparison of sequences of large size. Therefore, so-called alignment-free sequence comparison methods are needed for comparison between such as whole genome sequences in practical time. In this chapter, we reviewed the graphical representation of biological sequences, which is one of the major alignment-free sequence comparison methods. The notable effects of weighting during the course of the graphical representation introduced first by the author and co-workers were also mentioned.

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

Cited by 51 publications

References 18 publications

Using Huffman coding method to visualize and analyze DNA sequences

Using Huffman coding method to visualize and analyze DNA sequences

New graphical representation of a DNA sequence based on the ordered dinucleotides and its application to sequence analysis

Graphical Representation of Biological Sequences

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