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Reaction information supplementing method for KEGG database

A database and reaction technology, applied in the field of bioinformatics biological data analysis, can solve problems such as unmatched response subsystem information, missing main reaction, pathway information, inaccuracy, etc., to facilitate simulation and biological analysis, biological analysis The result is precise and credible, and the effect of reflecting comprehensive information

Active Publication Date: 2020-02-14
TIANJIN NORMAL UNIVERSITY
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Problems solved by technology

However, in these reaction information, there are problems such as the non-conservation of the elements on the left and right sides of the reaction equation, the lack of main reaction and pathway information in some reactions, and the mismatch of subsystem information in the reaction, which leads to the subsequent use of these reactions for pathway analysis, computer simulation calculation and biological characteristic analysis. There are certain difficulties and inaccuracies in

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  • Reaction information supplementing method for KEGG database

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Embodiment 1

[0023] Example 1 Supplementary information on the genome-scale metabolic network of Eriocheir sinensis

[0024] This method has been applied to the information supplementation of the genome-scale metabolic network of Eriocheir sinensis. In the preliminary research of the laboratory, combined with the reaction information data downloaded from the KEGG database and the transcriptome data of the Chinese mitten crab, a genome-scale metabolic network of the Chinese mitten crab was preliminarily constructed, and the network contained 1759 reactions and related information. Using the method described in this patent, the response information existing in the genome-scale metabolic network of the Chinese mitten crab is supplemented. The specific methods and results are as follows:

[0025] 1. Balance the reaction equation:

[0026] By counting the number of compound elements, splitting the reaction equation in the genome-scale metabolic network network model of Eriocheir sinensis, and...

Embodiment 2

[0033] Example 2 Supplementary Information of Litopenaeus vannamei Genome-Scale Metabolic Network

[0034] This method has been applied to the information supplementation of the genome-scale metabolic network of Litopenaeus vannamei. In the preliminary research of the laboratory, combined with the reaction information data downloaded from the KEGG database and the transcriptome data of Litopenaeus vannamei, a genome-scale metabolic network of Litopenaeus vannamei was preliminarily constructed, and the network contained 1690 reactions and related information. Using the method described in this patent, the response information existing in the genome-scale metabolic network of Litopenaeus vannamei is supplemented. The specific methods and results are as follows:

[0035] 1. Balance the reaction equation:

[0036] By counting the number of compound elements, splitting the reaction equations in the genome-scale metabolic network model of Litopenaeus vannamei, and counting the num...

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Abstract

The invention relates to the field of bioinformatics biological data analysis, and discloses a reaction information supplement method for a KEGG database. The technology is divided into four parts: reaction equation balancing, main reaction supplementing, path information supplementing and subsystem information supplementing. The reaction information data downloaded from the KEGG database has certain deficiency and omission, and part of the data information in the reaction information data can be supplemented through the method, so that the reaction information is more perfect and comprehensive. Network information is more complete, and subsequent simulation and biological analysis are facilitated.

Description

technical field [0001] The invention relates to the field of bioinformatics biological data analysis, in particular to a method for supplementing reaction information of a KEGG database. Background technique [0002] The continuous development of bioinformatics and database technology provides great convenience for researchers to collect and integrate huge data and efficiently use them to solve biological problems. In 1995, Kyoto University in Japan created the first relatively comprehensive metabolic database - KEGG (Kyoto Encyclopedia of Genes and Genomes) database, which collects sequence information of sequenced species and provides corresponding functional annotations. It is an integrated genome , a database of chemical and systemic functional information. So far, the KEGG database is constantly expanding, maintaining and correcting data, providing researchers with the latest metabolic information. [0003] Although the KEGG database is one of the most commonly used b...

Claims

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Application Information

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IPC IPC(8): G16C20/90G16C20/62
CPCG16C20/90G16C20/62
Inventor 郝彤孙金生赵凌轩
Owner TIANJIN NORMAL UNIVERSITY
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