Novel Protein Sequence Comparison Method Based on Transition Probability Graph and Information Entropy

(E-pub Ahead of Print)

Author(s): Zhaohui Qi*, Xinlong Wen

Journal Name: Combinatorial Chemistry & High Throughput Screening
Accelerated Technologies for Biotechnology, Bioassays, Medicinal Chemistry and Natural Products Research

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Abstract:

Aim and Objective: Sequence analysis is one of the foundations in bioinformatics. It is widely used to find out the feature metric hidden in the sequence. Otherwise, the graphical representation of biologic sequence is an important tool for sequencing analysis. This study is undertaken to find out a new graphical representation of biosequences.

Materials and Methods: The transition probability is used to describe amino acid combinations of protein sequences. The combinations are composed of amino acids directly adjacent to each other or separated by multiple amino acids. The transition probability graph is built up by the transition probabilities of amino acid combinations. Next, a map is defined as a representation from transition probability graph to transition probability vector by k-order transition probability graph. Transition entropy vectors are developed by the transition probability vector and information entropy. Finally, the proposed method is applied to two separate applications, 499 HA genes of H1N1, and 95 coronaviruses.

Results: By constructing a phylogenetic tree, we find that the results of each application are consistent with other studies.

Conclusion: the graphical representation proposed in this article is a practical and correct method.

Keywords: Graphical bioinfomatics, similarity, sequence, descriptors, transition prbability graph, information entropy.

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Article Details

(E-pub Ahead of Print)
DOI: 10.2174/1386207323666200901103001
Price: $95

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