Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation

Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation

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Sequence comparison is one of the foundations in bioinformatics, which can be used to study evolutionary relations among the sequences. In this study, a 2D spectrum-like graphical representation of protein sequences is presented based on the hydrophobicity scale of amino acids. The frequencies of am...

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Main Authors: Yuhua Yao, Shoujiang Yan, Huimin Xu, Jianning Han, Xuying Nan, Ping-an He, Qi Dai
Format: Article
Language:English
Published: SAGE Publishing 2014-01-01
Series:Evolutionary Bioinformatics
Online Access:https://doi.org/10.4137/EBO.S14713
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spelling doaj-0728941eef934967b44518c2f96755732020-11-25T03:12:30ZengSAGE PublishingEvolutionary Bioinformatics1176-93432014-01-011010.4137/EBO.S14713Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical RepresentationYuhua Yao0Shoujiang Yan1Huimin Xu2Jianning Han3Xuying Nan4Ping-an He5Qi Dai6College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.Sequence comparison is one of the foundations in bioinformatics, which can be used to study evolutionary relations among the sequences. In this study, a 2D spectrum-like graphical representation of protein sequences is presented based on the hydrophobicity scale of amino acids. The frequencies of amplitudes of 4-subsequences are adopted to characterize a spectrum-like graph, and a 17D vector is used as the descriptor of protein sequence. The Ç 2 value of compatibility test is performed. New similarity analysis approach is illustrated on the all protein sequences, which are encoded by the mitochondrion genome of 20 different species. Finally, comparison with the ClustalW method shows the utility of our method.https://doi.org/10.4137/EBO.S14713
collection DOAJ
language English
format Article
sources DOAJ
author Yuhua Yao
Shoujiang Yan
Huimin Xu
Jianning Han
Xuying Nan
Ping-an He
Qi Dai
spellingShingle Yuhua Yao
Shoujiang Yan
Huimin Xu
Jianning Han
Xuying Nan
Ping-an He
Qi Dai
Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation
Evolutionary Bioinformatics
author_facet Yuhua Yao
Shoujiang Yan
Huimin Xu
Jianning Han
Xuying Nan
Ping-an He
Qi Dai
author_sort Yuhua Yao
title Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation
title_short Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation
title_full Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation
title_fullStr Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation
title_full_unstemmed Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation
title_sort similarity/dissimilarity analysis of protein sequences based on a new spectrum-like graphical representation
publisher SAGE Publishing
series Evolutionary Bioinformatics
issn 1176-9343
publishDate 2014-01-01
description Sequence comparison is one of the foundations in bioinformatics, which can be used to study evolutionary relations among the sequences. In this study, a 2D spectrum-like graphical representation of protein sequences is presented based on the hydrophobicity scale of amino acids. The frequencies of amplitudes of 4-subsequences are adopted to characterize a spectrum-like graph, and a 17D vector is used as the descriptor of protein sequence. The Ç 2 value of compatibility test is performed. New similarity analysis approach is illustrated on the all protein sequences, which are encoded by the mitochondrion genome of 20 different species. Finally, comparison with the ClustalW method shows the utility of our method.
url https://doi.org/10.4137/EBO.S14713
work_keys_str_mv AT yuhuayao similaritydissimilarityanalysisofproteinsequencesbasedonanewspectrumlikegraphicalrepresentation
AT shoujiangyan similaritydissimilarityanalysisofproteinsequencesbasedonanewspectrumlikegraphicalrepresentation
AT huiminxu similaritydissimilarityanalysisofproteinsequencesbasedonanewspectrumlikegraphicalrepresentation
AT jianninghan similaritydissimilarityanalysisofproteinsequencesbasedonanewspectrumlikegraphicalrepresentation
AT xuyingnan similaritydissimilarityanalysisofproteinsequencesbasedonanewspectrumlikegraphicalrepresentation
AT pinganhe similaritydissimilarityanalysisofproteinsequencesbasedonanewspectrumlikegraphicalrepresentation
AT qidai similaritydissimilarityanalysisofproteinsequencesbasedonanewspectrumlikegraphicalrepresentation
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