Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation

Yao, Yao; Dai, Qi; Li, Ling; Nan, Xuying; He, Ping‐an; Zhang, Yaozhou

doi:10.1002/jcc.21391

Cited by 41 publications

(15 citation statements)

References 50 publications

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“…Graphic mapping of biological data, a powerful tool, has been employed to help people gain a useful insights by an intuitive manner (Randic et al 2003BielinskaWaz et al, 2007;Qi & Fan 2007;Novic & Randic 2008;Chou & Shen 2009;Bielinska-Waz 2010;Chou, 2010;Yao et al 2010;). Here we first used MUSCLE program (Edgar 2004) to do a multi-alignment of all analyzed sequences to get the identical residue position of each sequences.…”

Section: Methodsmentioning

confidence: 99%

Evolution trends of the 2009 pandemic influenza A (H1N1) viruses in different continents from March 2009 to April 2012

2014

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The World Health Organization (WHO) announced that the 2009 pandemic influenza A (H1N1) viruses, A/California/07/2009 (H1N1) — like virus, has gone into the post-pandemic period on August 10, 2010. People still have some concerns the virus would likely mutate and become a new pandemic virus in the future. Here, we use MUSCLE program and graphic mapping method to look into the evolutionary characteristics of the 6219 hemagglutinin and 4860 neuraminidase full-length sequences from March 2009 to April 2012. The graphic and statistical analyses showed that the novel pandemic isolates, A/California/07/2009 (H1N1) — like virus, experienced several different times. During the early-pandemic period (03/2009-08/2009), the viruses have spread globally in several clusters and deviated slightly from the recommended vaccine strain, A/California/07/2009. During the pandemic period (09/2009-08/2010), new clusters began to emerge from Asia and North America, and further deviated from the recommended vaccine strain. During the postpandemic period (09/2010-08/2011) and the recent period (09/2011-04/2012), the original cluster with the recommended vaccine isolate, A/California/07/2009, has nearly disappeared. The deviation degree between the new clusters and the vaccine isolate became larger and larger. However, the deviation degree and the deviation speed were low. The WHO did not choose a new vaccine isolate instead of the original vaccine isolate, A/California/07/2009. Even so, it is necessary to monitor continuously the 2009 pandemic influenza A (H1N1) viruses.

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Section: Methodsmentioning

confidence: 99%

Evolution trends of the 2009 pandemic influenza A (H1N1) viruses in different continents from March 2009 to April 2012

2014

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“…Graphical representation of protein sequences is a very powerful tool for visual comparison of protein sequences (Yao et al, 2010;Wang et al, 2014;2015). Currently, many effective graphical presentation methods have been proposed to facilitate the analysis of similarities/dissimilarities among the protein sequences.…”

Section: Introductionmentioning

confidence: 99%

A Novel 2D Graphical Representation and Its Application in the Similarities/Dissimilarities Analysis of Protein Sequences

Zhu¹

2016

American Journal of Biochemistry and Biotechnology

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In this study, a novel 2D graphical representation of protein sequences is proposed based on the physicochemical feature pK2 of amino acids first and then, on the basis of the newly given 2D graphical representation, a new concept of feature appearance model is introduced to analyze the similarity/dissimilarity of protein sequences. Finally, Theoretical and simulation results show that the newly proposed method is effective in similarities/dissimilarities analysis of protein sequences.

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“…The first visualization protein model was proposed by Randić et al until 2004 [19]. Some researchers have studied on graphical representation of protein sequences from different perspectives [20][21][22][23][24][25][26][27][28][29].…”

Section: Introductionmentioning

confidence: 99%

DV-Curve Representation of Protein Sequences and Its Application

Deng

Luan

2014

Computational and Mathematical Methods in Medicine

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Based on the detailed hydrophobic-hydrophilic(HP) model of amino acids, we propose dual-vector curve (DV-curve) representation of protein sequences, which uses two vectors to represent one alphabet of protein sequences. This graphical representation not only avoids degeneracy, but also has good visualization no matter how long these sequences are, and can reflect the length of protein sequence. Then we transform the 2D-graphical representation into a numerical characterization that can facilitate quantitative comparison of protein sequences. The utility of this approach is illustrated by two examples: one is similarity/dissimilarity comparison among different ND6 protein sequences based on their DV-curve figures the other is the phylogenetic analysis among coronaviruses based on their spike proteins.

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Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation

Cited by 41 publications

References 50 publications

Evolution trends of the 2009 pandemic influenza A (H1N1) viruses in different continents from March 2009 to April 2012

Evolution trends of the 2009 pandemic influenza A (H1N1) viruses in different continents from March 2009 to April 2012

A Novel 2D Graphical Representation and Its Application in the Similarities/Dissimilarities Analysis of Protein Sequences

DV-Curve Representation of Protein Sequences and Its Application

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