A new graphical representation of protein sequences and its applications

Hou, Wenbing; Pan, Qiuhui; He, Mingfeng

doi:10.1016/j.physa.2015.10.067

Cited by 17 publications

(10 citation statements)

References 24 publications

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“…If the points are all around the trend line, this shows that the correlation is better. Observing the figure, our method presented higher correlation with Clustal W than the methods of Hou et al, 5 Elmaatv et al, 6 Wen et al method, 7 Zhang et al method, 8 Wu et al, 9 Yao et al, 10 and He et al 14 …”

mentioning

confidence: 65%

“…Besides, comparing with other methods, our method analyzes similarity/dissimilarity of protein sequences based on nine properties, rather than two or three. For example, Hou et al 5 consider two properties of amino acids as the descriptor to reflect the relation among different proteins, Elmaatv et al 6 provide the method for correlation analysis based on three physicochemical properties. Then the PCA-FFT is utilized for reducing the dimension and transforming the protein sequences into number series to the correlation analysis.…”

Section: The Phylogenetic Tree Of the Protein Sequences Based On The mentioning

confidence: 99%

“…Currently, many researchers have proposed different methods for the graphical representation of protein sequences, which is a very powerful tool for visual comparison of protein sequences. For example, Hou et al 5 outlined a 3D graphical representation based on the classification of amino acids by different physicochemical properties, and then computed the similarities among different protein sequences. Elmaatv et al 6 proposed a 3D graphical representation of protein sequences based on three physicochemical properties of amino acid side chains and calculated similarities among nine ND5 protein sequences.…”

Section: Introductionmentioning

confidence: 99%

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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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mentioning

confidence: 65%

Section: The Phylogenetic Tree Of the Protein Sequences Based On The mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

2017

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“…Recently, Hou and co-workers visualized protein sequence as a 3D model through a graphical representation approach. 38 In their approach, the physiochemical attributes of amino acids such as hydrophobicity and molecular mass were used as descriptors. We used this concept for our present study.…”

Section: Construction Of Protein Sequences As a 3d Modelmentioning

confidence: 99%

Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor

et al. 2021

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It is well known that cervical cancer poses the fourth most malignancy threat to women worldwide among all cancer types. There is a tremendous improvement in realizing the underlying molecular associations in cervical cancer. Several studies reported pieces of evidence for the involvement of various genes in the disease progression. However, with the ever-evolving bioinformatics tools, there has been an upsurge in predicting numerous genes responsible for cervical cancer progression and making it highly complex to target the genes for further evaluation. In this article, we prioritized the candidate genes based on the sequence similarity analysis with known cancer genes. For this purpose, we used the concept of the moment of inertia tensor, which reveals the similarities between the protein sequences more efficiently.Tensor for moment of inertia explores the similarity of the protein sequences based on the physicochemical properties of amino acids. From our analysis, we obtained 14 candidate cervical cancer genes, which are highly similar to known cervical cancer genes. Further, we analyzed the GO terms and prioritized these genes based on the number of hits with biological process, molecular functions, and their involvement in KEGG pathways. We also discussed the evidence-based involvement of the prioritized genes in other cancers and listed the available drugs for those genes.

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“…There are several papers based on representations under physio-chemical properties of amino acids. In the article [13], the authors first outline a 2-D graphical representation on a unit circle based on the physicochemical properties of amino acids, mainly the hydrophobicity properties. Anyway this gives the two dimensional coordinates (x, y) on the circle.…”

Section: Use Of Classified Groups In Protein Sequence Comparisonmentioning

confidence: 99%

A Critical Mathematical Review on Protein Sequence Comparison Using Physio-Chemical Properties of Amino Acids

2020

J Mol Genet

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A new graphical representation of protein sequences and its applications

Cited by 17 publications

References 24 publications

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

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

Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor

A Critical Mathematical Review on Protein Sequence Comparison Using Physio-Chemical Properties of Amino Acids

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