A novel descriptor of protein sequences and its application

Yao, Yao; Yan, Shoujiang; Han, Jianning; Dai, Qi; He, Ping‐an

doi:10.1016/j.jtbi.2014.01.001

Cited by 29 publications

(23 citation statements)

References 56 publications

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“…By using the tool, one can obtain a route to condense the information coded by DNA primary sequences into a set of invariants [1,2]. Early attempts towards graphical representations of DNA were made by Hamori and Ruskin in 1983 [3], Hamori in 1985 [4], and Gates in 1985 [5].…”

Section: Introductionmentioning

confidence: 99%

“…Afterwards, more graphical representations of DNA sequences were well developed by researchers [1,2,[6][7][8][9][10][11][12][13][14][15]. In comparison with DNA, graphical representations of proteins emerged only very recently [2,[16][17][18][19][20][21][22][23][24][25][26][27]. As a matter of fact, most of the graphical representations of DNA involve some degree of arbitrariness, such as the selection of directions to be assigned to individual bases.…”

Section: Introductionmentioning

confidence: 99%

“…It is found that reducing the alphabet or fixing the directions assigned to amino acid residues plays an important role in addressing this problem. For details, we refer to some recent publications [2,16,21,23,24,28].…”

Section: Introductionmentioning

confidence: 99%

“…These matrices include: The frequency matrix; Euclidean-distance matrix (ED); graph theoretical distance matrix (GD); line distance matrix (LD); quotient matrix (D/D, M/M, L/L); and their "higher order" matrices [1,2,12,13,20,21,27,29,30]. Among them, ED, GD, L/L, etc., are derived from a graphical representation.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Numerical Characterization of Protein Sequences Based on the Generalized Chou’s Pseudo Amino Acid Composition

Lin

2016

Applied Sciences

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Abstract:The technique of comparison and analysis of biological sequences is playing an increasingly important role in the field of Computational Biology and Bioinformatics. One of the key steps in developing the technique is to identify an appropriate manner to represent a biological sequence. In this paper, on the basis of three physical-chemical properties of amino acids, a protein primary sequence is reduced into a six-letter sequence, and then a set of elements which reflect the global and local sequence-order information is extracted. Combining these elements with the frequencies of 20 native amino acids, a (21 + λ) dimensional vector is constructed to characterize the protein sequence. The utility of the proposed approach is illustrated by phylogenetic analysis and identification of DNA-binding proteins.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Numerical Characterization of Protein Sequences Based on the Generalized Chou’s Pseudo Amino Acid Composition

Lin

2016

Applied Sciences

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“…Ma et al 16 introduced a graphical representation of protein based on a novel iterated function system. Yao et al 17 proposed a 3D graphical representation of protein sequences based on three kinds of physical-chemical properties of amino acids. For those existing graphical representations of protein sequences given above, the main drawbacks are that, the higher the dimension of the protein sequence graphs, the heavier the computation complexity, or the lower the recognition degree of the protein sequence graphs.…”

Section: Introductionmentioning

confidence: 99%

Similarities/Dissimilarities Analysis of Protein Sequences Based on Pca-FFT

2017

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In this paper, a novel method to analyze the similarity/dissimilarity of protein sequences based on Principal Component Analysis-Fast Fourier Transformation (PCA-FFT) is proposed, in which, the PCA is utilized to transform protein sequences into time series and the FFT is utilized to analyze the time series while considering them as signals. To test the effectiveness of our newly proposed method, it is applied to analyze the similarity/dissimilarity of 16 different ND5 protein sequences and 29 different spike protein sequences, respectively. Furthermore, the correlation analysis is presented for comparing with others methods, and the simulation results show that it has better performances in the aspects of computation complexity and recognition degree than some existing methods.

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A generalization of CGR representation for analyzing and comparing protein sequences

Dai

et al. 2016

Int. J. Quantum Chem.

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Based on three kinds of physiochemical properties of amino acids, twenty amino acids are divided into eight groups, and replaced at eight vertices of a cube. Then, we present a new way of generalized Chaos Game Representation (CGR) method to outline a dynamic 3D graphical representation called HPL curve. Furthermore, the mathematical descriptor is suggested to characterize the similarities/dissimilarities of two HPL curves. The usefulness of this approach can be illustrated by performing the comparison of sequences of ND6 proteins of eight species, as well as sequences of sixteen ND5 proteins. By the correlation analysis, ClustalW results were compared with our results and some other graphical representation results to demonstrate the effectiveness of our approach. © 2016 Wiley Periodicals, Inc.

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A novel descriptor of protein sequences and its application

Cited by 29 publications

References 56 publications

Numerical Characterization of Protein Sequences Based on the Generalized Chou’s Pseudo Amino Acid Composition

Numerical Characterization of Protein Sequences Based on the Generalized Chou’s Pseudo Amino Acid Composition

Similarities/Dissimilarities Analysis of Protein Sequences Based on Pca-FFT

A generalization of CGR representation for analyzing and comparing protein sequences

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