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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 similar pair (human, gorilla); (b) the ADLD of the dissimilar pair (human, opossum); (c) the ADLD of the dissimilar pair (human, gallus).
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fig7: (a) The ADLD of the similar pair (human, gorilla); (b) the ADLD of the dissimilar pair (human, opossum); (c) the ADLD of the dissimilar pair (human, gallus).

Mentions: From Table 6, we can obtain some similar pairs such as (fin-whale, blue-whale), (pi-chim, c-chim), (Human, c-chim), (cheep, goat), (human, pi-chim), and (hare, rabbit) and some dissimilar pairs such as (human, opossum) and (human, gallus), among the above given 16 ND5 proteins. From these similar/dissimilar pairs, we will choose three pairs including (human, gorilla), (human, opossum), and (human, gallus) as examples to further show the intuition and visuality of the ADLDs of these three protein sequence pairs. The ADLDs of these three similar/dissimilar pairs are illustrated in Figure 7, while letting δ = 3.


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 similar pair (human, gorilla); (b) the ADLD of the dissimilar pair (human, opossum); (c) the ADLD of the dissimilar pair (human, gallus).
© Copyright Policy
Related In: Results  -  Collection

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

fig7: (a) The ADLD of the similar pair (human, gorilla); (b) the ADLD of the dissimilar pair (human, opossum); (c) the ADLD of the dissimilar pair (human, gallus).
Mentions: From Table 6, we can obtain some similar pairs such as (fin-whale, blue-whale), (pi-chim, c-chim), (Human, c-chim), (cheep, goat), (human, pi-chim), and (hare, rabbit) and some dissimilar pairs such as (human, opossum) and (human, gallus), among the above given 16 ND5 proteins. From these similar/dissimilar pairs, we will choose three pairs including (human, gorilla), (human, opossum), and (human, gallus) as examples to further show the intuition and visuality of the ADLDs of these three protein sequence pairs. The ADLDs of these three similar/dissimilar pairs are illustrated in Figure 7, while letting δ = 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