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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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The phylogenetic tree of the 16 species based on the ADLDs based method.
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fig3: The phylogenetic tree of the 16 species based on the ADLDs based method.

Mentions: Obviously, only through observing the similarity/dissimilarity matrix illustrated in Table 6, we will find that it is not very convenient to distinguish the similarity/dissimilarity of protein sequences. Therefore, in order to show the similarity/dissimilarity of the protein sequences more vividly and intuitively, according to the similarity/dissimilarity matrix illustrated in Table 6, then we will construct the phylogenetic tree of the above 16 ND5 proteins through adopting the software MEGA 6.06 that is provided by Tamura et al. [41], and the result is illustrated in Figure 3.


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 16 species based on the ADLDs based method.
© Copyright Policy
Related In: Results  -  Collection

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

fig3: The phylogenetic tree of the 16 species based on the ADLDs based method.
Mentions: Obviously, only through observing the similarity/dissimilarity matrix illustrated in Table 6, we will find that it is not very convenient to distinguish the similarity/dissimilarity of protein sequences. Therefore, in order to show the similarity/dissimilarity of the protein sequences more vividly and intuitively, according to the similarity/dissimilarity matrix illustrated in Table 6, then we will construct the phylogenetic tree of the above 16 ND5 proteins through adopting the software MEGA 6.06 that is provided by Tamura et al. [41], and the result is illustrated in Figure 3.

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