Method for predicting microbial population sensing gene abundance

A quorum sensing and microorganism technology, applied in the field of microorganisms, to achieve the effect of enriching annotation results and improving annotation efficiency

Pending Publication Date: 2022-08-02
DALIAN UNIV OF TECH
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Problems solved by technology

[0004] The invention provides a method for predicting the abundance of microbial quorum sensing-related genes by using a database, so as to solve the technical problems of comparing and annotating quorum sensing target genes and providing assessment of microbial quorum sensing function-related capabilities

Method used

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  • Method for predicting microbial population sensing gene abundance
  • Method for predicting microbial population sensing gene abundance
  • Method for predicting microbial population sensing gene abundance

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Experimental program
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Embodiment 1

[0063] like figure 1 As shown, the present invention constructs a database process, and the specific steps are as follows:

[0064] S101. Search all literatures related to quorum sensing in the PubMed database of the National Center for Biotechnology Information (NCBI).

[0065] For the quorum sensing literature library involved in the present invention, all literatures related to the keyword "quorum" were retrieved from the PubMed database in NCBI, and as of October 30, 2021, a total of 12,596 literatures were collected.

[0066] S102, using Endnote software to manually classify the literature, and finally form a quorum sensing literature library based on signals and corresponding genes, including 6 kinds of signal molecules and 24 kinds of related genes related to them.

[0067] as attached figure 2 As shown in the screenshot of the document index database of the present invention, after removing 2167 irrelevant documents and classifying them according to signal molecules...

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Abstract

The invention provides a method for predicting microbial quorum sensing gene abundance. The method comprises the following steps: S1, establishing a quorum sensing literature index database; s2, establishing a quorum sensing sequence database; s3, constructing a hidden Markov model of a protein conserved site; s4, counting a sequence recovery number and a gene recovery rate corresponding to the gene, and constructing a standardized database; s5, predicting the abundance of the microbial population sensing gene; according to the method for predicting the abundance of the microbial quorum sensing related genes by using the hidden Markov model, more comprehensive quorum sensing related genes in a microbial community can be annotated through the constructed database, the method can be further applied to an environmental sample, and the quorum sensing target genes are compared and annotated, so that the accuracy of the quorum sensing related genes is improved. The method can be used for evaluating homology comparison and annotation of a target protein, is further used for performing homology comparison and annotation on a target gene in an actual environment sample, and provides predictive analysis of microbial population sensing signal generation, sensing and quenching capabilities.

Description

technical field [0001] The present invention relates to the technical field of microorganisms, and more particularly, to a method for predicting the abundance of quorum sensing genes in microorganisms. Background technique [0002] Bacteria were once generally considered to be simple cellular life with only a single physiological behavior, but more and more studies have confirmed that bacteria have multicellular swarm cooperative behavior. These synergistic behaviors include processes such as bioluminescence, production of virulence factors, production of secondary metabolites, gene upregulation, and biofilm formation. These processes often require individual cells to coordinate within a population. In order to better coordinate the behavior of groups, bacteria utilize a process of cell-to-cell communication known as quorum sensing. The quorum sensing signals that have been identified are mainly acyl homoserine lactones (HSLs), other autoinducers 2 (AI-2), diffusible signa...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10G16B50/00G06K9/62G06F16/9035
CPCG16B30/10G16B50/00G06F16/9035G06F18/23G06F18/241Y02A90/10
Inventor 曲媛媛戴春晓荆佳维吴炜泽陈卓杨颖赵博谭佳金延铭
Owner DALIAN UNIV OF TECH
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