Application of 2D graphic representation of protein sequence based on Huffman tree method

Zhang, Qi; Feng, Jufu; Qi, Xiao-Qin; Li, Ling

doi:10.1016/j.compbiomed.2012.01.011

Cited by 17 publications

(12 citation statements)

References 31 publications

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“…Currently, many researchers have proposed different methods for the graphical representation of protein sequences [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24]. For example, Feng and Zhang [25] suggested Zp-curve based on the hydrophobicity and charged properties of amino acid residues along the primary sequence.…”

Section: Introductionmentioning

confidence: 99%

ADLD: A Novel Graphical Representation of Protein Sequences and Its Application

Wang

Peng

Zheng

2014

Computational and Mathematical Methods in Medicine

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To facilitate the intuitional analysis of protein sequences, a novel graphical representation of protein sequences called ADLD (Alignment Diagonal Line Diagram) is introduced in this paper first, and then a new ADLD based method is proposed and utilized to analyze the similarity/dissimilarity of protein sequences. Comparing with existing methods, our ADLD based method is proved to be effective in the similarity/dissimilarity analysis of protein sequences and have the merits of good intuition, visuality, and simplicity. The examinations of the similarities/dissimilarities for both the 16 different ND5 proteins and the 29 different spike proteins illustrate the utility of our ADLD based approach.

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Section: Introductionmentioning

confidence: 99%

ADLD: A Novel Graphical Representation of Protein Sequences and Its Application

Wang

Peng

Zheng

2014

Computational and Mathematical Methods in Medicine

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“…Then in Gates, 21 Nandy,22 and Leong, 23 authors presented an original plot of a DNA sequences. By a random walk on a 2D grid the plot used the four cardinal directions to represent the four bases: A, G, T and C. In recent ten years, some authors such as, Randić,[24][25][26][27] Bielińska-Wąż, 28 29 Novic, 30 Jaklic, 31 Yao, 32-34 Qi, [35][36][37][38] Zhang 39 and Huang, 40 also presented their graphic representations of DNA or protein sequences. Some graphic methods visualizing DNA sequences provide useful insights about * Author to whom correspondence should be addressed.…”

Section: Introductionmentioning

confidence: 98%

“…In addition, as for a type of alignmentfree method, some graphic methods for DNA sequence are also used to make genome comparison, such as Ref. [38]. The alignment-free methods are some schemes without insertions/deletions.…”

Section: Introductionmentioning

confidence: 99%

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Graphic Mapping of Protein-Coding DNA Sequence in Four-Dimensional Space and its Application

Qi¹,

Li²,

Zhang³

2014

Jnl of Comp & Theo Nano

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We propose a graphic mapping method of protein-coding DNA sequence in four-dimensional (4D) space. The proposed graphic method considers both nucleotide and amino acid information in protein-coding DNA sequences simultaneously. Based on the graphic mapping, a 48-dimensional (48D) vector set and its mean value are used to describe the statistical characteristics of genome. Then, we use the proposed method to analyze a typical biological data set, 31 mitochondrial genomes analyzed by alignment-free methods. The results show that the proposed method can distinguish characteristics of different genomes and be used to reconstruct the phylogenetic tree of different genomes.

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“…Huang et al (2013) introduced a 2D graphical representation of protein sequence, called HR-Curve, based on classification and dual vectors. Qi et al (2012) proposed a 2D graphical representation of protein sequence based on Huffman tree. Abo-Elkhier (2012) proposed a 3D graphical representation of protein sequence on the basis of a right cone of a unit base and unit height on protein sequences interfaces.…”

Section: Introductionmentioning

confidence: 99%

A Novel 2D Graphical Representation and Its Application in the Similarities/Dissimilarities Analysis of Protein Sequences

Zhu¹

2016

American Journal of Biochemistry and Biotechnology

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In this study, a novel 2D graphical representation of protein sequences is proposed based on the physicochemical feature pK2 of amino acids first and then, on the basis of the newly given 2D graphical representation, a new concept of feature appearance model is introduced to analyze the similarity/dissimilarity of protein sequences. Finally, Theoretical and simulation results show that the newly proposed method is effective in similarities/dissimilarities analysis of protein sequences.

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Application of 2D graphic representation of protein sequence based on Huffman tree method

Cited by 17 publications

References 31 publications

ADLD: A Novel Graphical Representation of Protein Sequences and Its Application

ADLD: A Novel Graphical Representation of Protein Sequences and Its Application

Graphic Mapping of Protein-Coding DNA Sequence in Four-Dimensional Space and its Application

A Novel 2D Graphical Representation and Its Application in the Similarities/Dissimilarities Analysis of Protein Sequences

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