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Method for rebuilding species system generation tree based on alignment of multiple metabolic pathways

A phylogenetic tree and path technology, applied in biological systems, evolutionary organisms, bioinformatics, etc., can solve problems such as limited node mapping information

Active Publication Date: 2017-06-30
GUANGXI UNIV
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Problems solved by technology

However, the mapping information between nodes is limited, and it is difficult to dig deeper into the relationship between metabolic pathways only through node mapping information

Method used

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  • Method for rebuilding species system generation tree based on alignment of multiple metabolic pathways
  • Method for rebuilding species system generation tree based on alignment of multiple metabolic pathways
  • Method for rebuilding species system generation tree based on alignment of multiple metabolic pathways

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Embodiment Construction

[0040] The method of reconstructing the phylogenetic tree of species based on the comparison of multiple metabolic pathways, the specific steps are as follows:

[0041] 1) Establishment of multiple metabolic pathway composite maps:

[0042] 1.1) Calculation of node similarity:

[0043] For the metabolic pathway P, let G p =(V p ,E p ) represents the metabolic pathway P, where G p is a directed graph, V p is G p The vertex set of E p is G p The set of directed edges, G p Vertex u in i and u j Denotes the reaction r in P i and r j . if r i One of the output compounds is r j an input compound of , then u i and u j There exists a line from r i to r j The directed edge, if r i , r j are reversible, then there is also a path from r j to r i The directed edge of .

[0044] k is a positive integer, for graph G p For any node u in , define the set of k neighbors of u: N k (u),N k (u) is V p A set of nodes for which u does not belong to N k (u) and for any x...

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Abstract

The invention discloses a method for rebuilding a species system generation tree based on alignment of multiple metabolic pathways. The method comprises the following steps: building a combined graph of the multiple metabolic pathways through global alignment of the multiple metabolic pathways, then building mapping between functional modules of all the metabolic pathways through node clustering of the combined graph, further analyzing a relation among the metabolic pathways according to the mapping of the functional modules, and building the system generation tree among species. The method has the beneficial effects that by the implementation of the method, the alignment work of the metabolic pathways is simplified, and a researcher only needs to do simple operation to quickly and accurately generate the system generation tree among the species.

Description

technical field [0001] The method relates to a method for generating a species phylogenetic tree. Specifically, it is a method for generating a species phylogenetic tree based on the comparison of multiple metabolic pathways. Background technique [0002] Phylogenetic analysis is an important field of systems biology research. The current method of using metabolic data to build a phylogenetic tree mainly analyzes the relationship between metabolic pathways through the mapping between metabolic pathway nodes, and uses these relationships to systematically analyze species. Analysis occurs. However, the mapping information between nodes is limited, and it is difficult to dig deeper into the relationship between metabolic pathways only through node mapping information. Contents of the invention [0003] The purpose of the present invention is to provide a method for establishing a phylogenetic tree among species based on the comparison of multiple metabolic pathways. [000...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/14G06F19/12G16B10/00
CPCG16B5/00G16B10/00
Inventor 黄毅然钟诚林海翔
Owner GUANGXI UNIV
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