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A method for automatic correction of genome metabolic network model

A metabolic network and genome technology, which is applied in the field of automatic correction of genome metabolic network models, can solve problems such as the inability to provide reaction interval positioning, and achieve a comprehensive effect of correcting the model.

Active Publication Date: 2017-05-10
广州市康伦生物技术有限公司
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Problems solved by technology

Model SEED and Pathway Tools can only provide the refining automation process of the prokaryotic metabolic network model, but cannot provide the positioning of the reaction interval

Method used

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  • A method for automatic correction of genome metabolic network model
  • A method for automatic correction of genome metabolic network model
  • A method for automatic correction of genome metabolic network model

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Experimental program
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Embodiment Construction

[0046] The present invention will be further described below in conjunction with embodiment.

[0047] Taking the correction process of the rough model of the Spathaspora passalidarum NRRL Y-27907 genome as an example to illustrate, the loopholes in the rough model are automatically filled in, and the direction of the reaction and the interval of the reaction are determined. Specific steps are as follows:

[0048] 1. According to the list of vulnerable metabolites returned by matlab, fill in the specific reaction of Spathaspora passalidarum NRRL Y-27907. figure 1 It is the flow chart of step 1, which shows the process of auto-filling breakpoints, and provides an intuitive description of the process of auto-filling breakpoints in the form of program flow, and can be accessed fromfigure 1 See the process of cyclically judging each compound and each reaction in turn.

[0049] (1A), import the rough model of genome metabolic network into the matlab software equipped with cobra too...

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Abstract

The invention discloses an automatic genomic metabolic network model modifying method. According to the automatic genomic metabolic network model modifying method, website script semanteme can be submitted and analyzed automatically by combining a hypertext transfer protocol with a Java control HttpClient and utilizing an image processing algorithm; a genomic metabolic network model is subjected to automatic breakpoint supplementing on the basis of online databases including a KEGG (Kyoto Encyclopedia of Genes and Genomes) database, a MetaCyc database, a MetRxn database and a plurality of protein region positioning and predicting websites; specific reactions high in reliability can be determined according to a protein region predicting result and a weight rating mechanism, and accordingly, an automatic modifying process of a rough metabolic network model is completed. The automatic genomic metabolic network model modifying method has the advantages of time saving and convenience, and an obtained modified model is more comprehensive and more accurate.

Description

technical field [0001] The invention belongs to the field of bioinformatics, and specifically relates to a method for automatically correcting a genome metabolic network model by using a computer to mine biological information data and using an image processing algorithm and a weight scoring mechanism. Background technique [0002] With the emergence of high-throughput genome sequencing data and the generation of a large amount of biological data, the construction of genomic metabolic network models has become one of the hotspots of research. Metabolic network construction is a labor-intensive and time-consuming process, so a large number of automated construction tools have emerged. Usually, these automated tools focus on the construction and simulation process of the rough model of the metabolic network, and only a small number of automated tools are aimed at the correction process of the metabolic network model. Currently, the tools that can provide the automatic refinin...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/12
Inventor 张梁吴晓红薛卫李由然李赢丁重阳石贵阳
Owner 广州市康伦生物技术有限公司
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