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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 ADLD of the protein sequence pair (chimpanzee, human); (b) the ADLD of the protein sequence pair (human, gorilla).
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fig2: (a) The ADLD of the protein sequence pair (chimpanzee, human); (b) the ADLD of the protein sequence pair (human, gorilla).

Mentions: According to the above assumptions, in Figure 2, we show the two ADLDs corresponding to the ASDs illustrated in Figures 1(a) and 1(b) while letting δ = 3. And, in addition, to make the ADLDs more visual and intuitional, in Figure 2, we use the red “∗” to represent the FPs on the AT and the blue lines to represent the SFs on the AT or BTs.


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

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

(a) The ADLD of the protein sequence pair (chimpanzee, human); (b) the ADLD of the protein sequence pair (human, gorilla).
© Copyright Policy
Related In: Results  -  Collection

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

fig2: (a) The ADLD of the protein sequence pair (chimpanzee, human); (b) the ADLD of the protein sequence pair (human, gorilla).
Mentions: According to the above assumptions, in Figure 2, we show the two ADLDs corresponding to the ASDs illustrated in Figures 1(a) and 1(b) while letting δ = 3. And, in addition, to make the ADLDs more visual and intuitional, in Figure 2, we use the red “∗” to represent the FPs on the AT and the blue lines to represent the SFs on the AT or BTs.

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