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A Fractal Dimension and Wavelet Transform Based Method for Protein Sequence Similarity Analysis
Lina Yang; Yuan Yan Tang; Yang Lu; Huiwu Luo
2015-03-01
Source PublicationIEEE/ACM Transactions on Computational Biology and Bioinformatics
ISSN1545-5963
Volume12Issue:2Pages:348-359
Abstract

One of the key tasks related to proteins is the similarity comparison of protein sequences in the area of bioinformatics and molecular biology, which helps the prediction and classification of protein structure and function. It is a significant and open issue to find similar proteins from a large scale of protein database efficiently. This paper presents a new distance based protein similarity analysis using a new encoding method of protein sequence which is based on fractal dimension. The protein sequences are first represented into the 1-dimensional feature vectors by their biochemical quantities. A series of Hybrid method involving discrete Wavelet transform, Fractal dimension calculation (HWF) with sliding window are then applied to form the feature vector. At last, through the similarity calculation, we can obtain the distance matrix, by which, the phylogenic tree can be constructed. We apply this approach by analyzing the ND5 (NADH dehydrogenase subunit 5) protein cluster data set. The experimental results show that the proposed model is more accurate than the existing ones such as Su's model, Zhang's model, Yao's model and MEGA software, and it is consistent with some known biological facts.

KeywordDiscrete Wavelet Transform Fractal Dimension Higuchi's Algorithm Protein Sequence Similarity Sliding Window
DOIhttps://doi.org/10.1109/TCBB.2014.2363480
URLView the original
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Computer Science ; Mathematics
WOS SubjectBiochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability
WOS IDWOS:000352788300010
PublisherIEEE COMPUTER SOC, 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1314 USA
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Cited Times [WOS]:5   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionDEPARTMENT OF COMPUTER AND INFORMATION SCIENCE
Corresponding AuthorLina Yang; Yuan Yan Tang; Yang Lu; Huiwu Luo
AffiliationDepartment of Computer and Information Science, Faculty of Science and Technology, University of Macau, 999078 Macau.
First Author AffilicationFaculty of Science and Technology
Corresponding Author AffilicationFaculty of Science and Technology
Recommended Citation
GB/T 7714
Lina Yang,Yuan Yan Tang,Yang Lu,et al. A Fractal Dimension and Wavelet Transform Based Method for Protein Sequence Similarity Analysis[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics,2015,12(2):348-359.
APA Lina Yang,Yuan Yan Tang,Yang Lu,&Huiwu Luo.(2015).A Fractal Dimension and Wavelet Transform Based Method for Protein Sequence Similarity Analysis.IEEE/ACM Transactions on Computational Biology and Bioinformatics,12(2),348-359.
MLA Lina Yang,et al."A Fractal Dimension and Wavelet Transform Based Method for Protein Sequence Similarity Analysis".IEEE/ACM Transactions on Computational Biology and Bioinformatics 12.2(2015):348-359.
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