A method and system for constructing a microbial gene database

A construction method and database technology, applied in bioinformatics, instruments, etc., can solve the problems of large number of genes, low accuracy, and many types of annotated microorganisms, and achieve accurate classification information, reliable comparison results, and convenient update and iteration Effect

Active Publication Date: 2022-07-01
SHENZHEN AIMIGENE TECH CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

IGC has the following problems: (1) the number of genes is large, there are many types of annotated microorganisms, and the comparison time is very long, and the efficiency is low; (2) the gene annotation information has not been updated for a long time, and the accuracy is low; (3) the public gene annotation The information is only at the genus level, and the target probiotics cannot be analyzed
Although MetaPhlAn has been updated all the time, it also has the following limitations: (1) Using sequence alignment marker genes to obtain relative abundance information, compared with other strategies, the false positives are lower, but the read utilization rate is low; (2) ) Fewer species are detected, and only species in the database can be detected; (3) Species are annotated only at the species level, and the strain-level results need to be analyzed using the supporting StrainPhlAn tool
However, the traditional method of directly constructing the genome of probiotics as a reference database will have a large amount of repetitive information, resulting in low efficiency; in addition, since there are many common segments among microbial genomes, if the whole genome is directly used as a reference genome, it will also affect Accuracy of test results

Method used

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  • A method and system for constructing a microbial gene database
  • A method and system for constructing a microbial gene database
  • A method and system for constructing a microbial gene database

Examples

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Comparison scheme
Effect test

Embodiment 1

[0078] Example 1 Microbial gene database construction system

[0079] like figure 1 As shown, the present embodiment provides a construction system for a microbial gene database, that is, construction system #1 includes the following modules:

[0080] The genome data acquisition and storage module is used to acquire and store the genome data of each target microorganism in the target microorganism combination, wherein the target microorganism combination includes N kinds of target microorganisms, and N≥1;

[0081] The gene prediction module is connected with the genomic data acquisition and storage module, and is used to perform gene prediction on the genomic data acquired in the genomic data acquisition module, obtain and output gene annotation files including sequences and annotations;

[0082] a representative gene acquisition module, connected with the gene prediction module, for receiving the gene annotation file output by the gene prediction module, and using the gene ...

Embodiment 2

[0086] Microbial gene database construction system upgraded by embodiment 2

[0087] In this example, the construction system #1 of Example 1 is upgraded to obtain construction system #2. The improvement point is that it further includes a gene de-redundancy module, which is connected to the gene verification module and is used to receive the retained genes output by the gene verification module. , and use gene de-redundancy software to de-redundancy the retained genes, extract single-copy alignment genes, and obtain a non-redundant microbial gene database.

[0088] Wherein, the steps of extracting unit copy comparison genes are as follows:

[0089] For each species, perform de-redundancy separately: filter all the genes of the sequence class with the number of genes greater than 1, and all the remaining genes are the only aligned single-copy genes of the species;

[0090] The de-redundant genes of all species were merged, and all genes of the sequence class with gene number ...

Embodiment 3

[0091] The microbial gene database construction system that embodiment 3 upgrades

[0092] In this example, the construction system #1 of Example 1 or the construction system #2 of Example 2 are respectively upgraded to obtain the construction system #3 and construction system #4. The improvement points are: in the representative genome analysis module and the gene alignment module In between, a gene filtering module is further included, which is respectively connected with the representative gene acquisition module and the gene comparison module, and is used to receive the representative genes output by the representative gene acquisition module and filter: the genes whose sequence length is less than 200 are filtered, and then the filtered Represent gene output to the Gene Alignment module.

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Abstract

The invention discloses a method and system for constructing a microbial gene database, and belongs to the technical field of gene database construction. The method includes the following steps: obtaining target microorganism genome data, performing gene prediction on the obtained genome data, and obtaining a gene annotation file including sequence and species annotation; obtaining representative genes of each target microorganism; Each gene is aligned to the nucleic acid sequence database, and the alignment result is obtained; the alignment result is filtered to obtain the gene annotation species information, and the genes of the annotated species and the source species are retained, and then the microbial gene database is constructed. Using the construction method of the present invention to construct a microbial gene database, the database can be updated according to the changes of the target microorganism, and the real-time performance is stronger.

Description

technical field [0001] The invention belongs to the technical field of gene database construction, and in particular, relates to a method and system for constructing a microbial gene database. Background technique [0002] In recent years, with the deepening of human microbiome research, scientists have discovered that gut microbes play a significant role in promoting human health. Some current sub-health problems are also caused by the disruption of the balance of gut microecology. . As a type of microorganism beneficial to the human body, probiotics can well help restore the intestinal microecological balance, and have been widely used in dietary supplements. However, due to the wide variety of probiotics, different countries have issued corresponding policies to regulate the types of edible probiotics. [0003] The traditional research on microorganisms is to culture the microorganisms and then observe the biochemical phenotype, which takes dozens of days to complete. ...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B50/30G16B50/10
CPCG16B50/30G16B50/10
Inventor 徐晓强夏炎王晓凯谢海亮
Owner SHENZHEN AIMIGENE TECH CO LTD
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