A new approach to protein sequence visualization based on PCA with Fourier low-pass filter

Yi Liu

doi:10.1117/12.2669482

24 March 2023 A new approach to protein sequence visualization based on PCA with Fourier low-pass filter

Yi Liu

Proceedings Volume 12611, Second International Conference on Biological Engineering and Medical Science (ICBioMed 2022); 126110P (2023) https://doi.org/10.1117/12.2669482
Event: International Conference on Biological Engineering and Medical Science (ICBioMed2022), 2022, Oxford, United Kingdom

Abstract

In this paper, I applied principal component analysis to downscale the six physicochemical properties of amino acids to analyze their correlation and make a similarities/dissimilarities matrix corresponding to nine mammalian ND5 protein sequences based on the scores of amino acids to construct a phylogenetic tree. Meanwhile, a new method to observe protein sequence similarity and dissimilarity is proposed in this paper, using Fourier low-pass filter with 3D Smoother, to see the dissimilarities of different proteins more intuitively upfront.

Citation Download Citation

Yi Liu "A new approach to protein sequence visualization based on PCA with Fourier low-pass filter", Proc. SPIE 12611, Second International Conference on Biological Engineering and Medical Science (ICBioMed 2022), 126110P (24 March 2023); https://doi.org/10.1117/12.2669482

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KEYWORDS

Proteins

Linear filtering

Principal component analysis

Matrices

Animals

Visualization

Lithium

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