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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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(a) The ASD of the β-globin protein sequence pair (chimpanzee, human) with ξ = 12; (b) the ASD of the β-globin protein sequence pair (human, gorilla) with ξ = 16.
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fig1: (a) The ASD of the β-globin protein sequence pair (chimpanzee, human) with ξ = 12; (b) the ASD of the β-globin protein sequence pair (human, gorilla) with ξ = 16.

Mentions: For example, considering the three β-globin protein sequences of chimpanzee [GenBank: AAA16334.1], human [GenBank: CAA26204.1], and gorilla [GenBank: CAA43421.1] obtained from the GenBank, respectively, we illustrate the ASDs of the β-globin protein sequence pair (chimpanzee, human) and the β-globin protein sequence pair (human, gorilla) in Figures 1(a) and 1(b) separately while letting ε = 0.


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

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

(a) The ASD of the β-globin protein sequence pair (chimpanzee, human) with ξ = 12; (b) the ASD of the β-globin protein sequence pair (human, gorilla) with ξ = 16.
© Copyright Policy
Related In: Results  -  Collection

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

fig1: (a) The ASD of the β-globin protein sequence pair (chimpanzee, human) with ξ = 12; (b) the ASD of the β-globin protein sequence pair (human, gorilla) with ξ = 16.
Mentions: For example, considering the three β-globin protein sequences of chimpanzee [GenBank: AAA16334.1], human [GenBank: CAA26204.1], and gorilla [GenBank: CAA43421.1] obtained from the GenBank, respectively, we illustrate the ASDs of the β-globin protein sequence pair (chimpanzee, human) and the β-globin protein sequence pair (human, gorilla) in Figures 1(a) and 1(b) separately while letting ε = 0.

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