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ADLD: a novel graphical representation of protein sequences and its application.

Wang L, Peng H, Zheng J - Comput Math Methods Med (2014)

Bottom Line: To facilitate the intuitional analysis of protein sequences, a novel graphical representation of protein sequences called ADLD (Alignment Diagonal Line Diagram) is introduced in this paper first, and then a new ADLD based method is proposed and utilized to analyze the similarity/dissimilarity of protein sequences.Comparing with existing methods, our ADLD based method is proved to be effective in the similarity/dissimilarity analysis of protein sequences and have the merits of good intuition, visuality, and simplicity.The examinations of the similarities/dissimilarities for both the 16 different ND5 proteins and the 29 different spike proteins illustrate the utility of our ADLD based approach.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Intelligent Computing & Information Processing, Ministry of Education, Xiangtan University, Xiangtan 411105, China ; College of Information Engineering, Xiangtan University, Xiangtan 411105, China.

ABSTRACT
To facilitate the intuitional analysis of protein sequences, a novel graphical representation of protein sequences called ADLD (Alignment Diagonal Line Diagram) is introduced in this paper first, and then a new ADLD based method is proposed and utilized to analyze the similarity/dissimilarity of protein sequences. Comparing with existing methods, our ADLD based method is proved to be effective in the similarity/dissimilarity analysis of protein sequences and have the merits of good intuition, visuality, and simplicity. The examinations of the similarities/dissimilarities for both the 16 different ND5 proteins and the 29 different spike proteins illustrate the utility of our ADLD based approach.

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Related in: MedlinePlus

The phylogenetic tree of the 29 spike proteins of coronavirus constructed by adopting the ADLDs based method with δ = 5.
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fig4: The phylogenetic tree of the 29 spike proteins of coronavirus constructed by adopting the ADLDs based method with δ = 5.

Mentions: For the 29 spike proteins illustrated in Table 7, we construct the phylogenetic tree in Figure 4. Since the spike protein sequences are very long (with more than 1100 amino acids), therefore, during simulation, we set δ = 5 to avoid the effect of noise points.


ADLD: a novel graphical representation of protein sequences and its application.

Wang L, Peng H, Zheng J - Comput Math Methods Med (2014)

The phylogenetic tree of the 29 spike proteins of coronavirus constructed by adopting the ADLDs based method with δ = 5.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230005&req=5

fig4: The phylogenetic tree of the 29 spike proteins of coronavirus constructed by adopting the ADLDs based method with δ = 5.
Mentions: For the 29 spike proteins illustrated in Table 7, we construct the phylogenetic tree in Figure 4. Since the spike protein sequences are very long (with more than 1100 amino acids), therefore, during simulation, we set δ = 5 to avoid the effect of noise points.

Bottom Line: To facilitate the intuitional analysis of protein sequences, a novel graphical representation of protein sequences called ADLD (Alignment Diagonal Line Diagram) is introduced in this paper first, and then a new ADLD based method is proposed and utilized to analyze the similarity/dissimilarity of protein sequences.Comparing with existing methods, our ADLD based method is proved to be effective in the similarity/dissimilarity analysis of protein sequences and have the merits of good intuition, visuality, and simplicity.The examinations of the similarities/dissimilarities for both the 16 different ND5 proteins and the 29 different spike proteins illustrate the utility of our ADLD based approach.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Intelligent Computing & Information Processing, Ministry of Education, Xiangtan University, Xiangtan 411105, China ; College of Information Engineering, Xiangtan University, Xiangtan 411105, China.

ABSTRACT
To facilitate the intuitional analysis of protein sequences, a novel graphical representation of protein sequences called ADLD (Alignment Diagonal Line Diagram) is introduced in this paper first, and then a new ADLD based method is proposed and utilized to analyze the similarity/dissimilarity of protein sequences. Comparing with existing methods, our ADLD based method is proved to be effective in the similarity/dissimilarity analysis of protein sequences and have the merits of good intuition, visuality, and simplicity. The examinations of the similarities/dissimilarities for both the 16 different ND5 proteins and the 29 different spike proteins illustrate the utility of our ADLD based approach.

Show MeSH
Related in: MedlinePlus