Method of adopting firework algorithm to recognize protein complex

A technology of protein complex and fireworks algorithm, applied in the field of bioinformatics, can solve the problem of internal structure of protein complex and protein complex without considering the dynamics of protein interaction network and the inability to consider the global characteristics and local characteristics of protein interaction network at the same time. Problems such as low object recognition accuracy

Inactive Publication Date: 2016-12-14
SHAANXI NORMAL UNIV
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Problems solved by technology

[0010] The disadvantage of the above clustering method is that it does not take into account the dynamics of the protein interaction network, the global and local characteristics of th

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  • Method of adopting firework algorithm to recognize protein complex
  • Method of adopting firework algorithm to recognize protein complex
  • Method of adopting firework algorithm to recognize protein complex

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Embodiment Construction

[0057] The present invention will be described in further detail below in conjunction with the accompanying drawings and examples, but the present invention is not limited to these examples.

[0058] Such as figure 1 As shown, the method for identifying protein complexes using the fireworks algorithm of the present invention comprises the following steps:

[0059] (1) Transform the protein interaction network into an undirected graph

[0060] Transform the protein interaction network into an undirected graph G=(V,E), where V={v i ,i=1,2,…,n} is node v i The set of , E is the set of edge e, the node v i Represents proteins, edge e represents the interaction between proteins, w ij represents the node v i with node v j The connection between, if the node v i with node v j connected, then w ij = 1, if v i with v j There is no edge between them, then w ij =0, i=1,2,...,n, j=1,2,...,n;

[0061] (2) Preprocessing of edges and nodes in the protein interaction network

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Abstract

The invention provides a method of adopting a firework algorithm to recognize a protein complex. The method includes following steps: converting a protein interaction network into an undirected graph; pre-treating sides and nodes of the protein interaction network; building a dynamic protein interaction network; setting parameters; initializing positions of fireworks; simulating firework explosion to generate spark; selecting part of good points from the spark to serve as fireworks, wherein all fireworks form a class; filtering undesirable classes; outputting a finally-acquired class. The method takes dynamic nature of a protein network and locality and globality of a core-accessory structure inside the protein complex and the protein interaction network into consideration, and the protein complex can be recognized accurately. Simulation experiment results show that performance of indexes like accuracy and recall ratio is excellent. Compared with other clustering methods, the method has the advantages that characteristics of the protein interaction network and the protein complex are combined to recognize the protein complex, and recognition accuracy of the protein complex is improved.

Description

technical field [0001] The invention belongs to the field of biological information, and relates to a method for identifying protein complexes in a dynamic protein interaction network, in particular to a method for identifying protein complexes using a fireworks algorithm. Background technique [0002] With the completion of the Human Genome Project and the sequencing of multi-species genomes, the study of proteomics kicked off. Protein is an indispensable component of life and an important participant in ensuring the normal progress of life activities, and proteomics is to study the function, structure and interaction between proteins in order to fully describe the entire life cycle all proteins in . Every protein in a cell does not exist in isolation, and every life activity involves multiple proteins from the beginning to the end, and these proteins are connected together through interactions to complete a life activity. The interaction of proteins is also the guarantee...

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Application Information

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IPC IPC(8): G06F19/24
CPCG16B40/00
Inventor 雷秀娟王飞程适
Owner SHAANXI NORMAL UNIV
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