Construction method and system of 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: 2022-03-01
SHENZHEN AIMIGENE TECH CO LTD
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  • Abstract
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  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

This patented technology allows for quicker access to large amounts of complex DNA from various sources such as soil samples that may contain harmful organics. It also includes an efficient way to compare unknown strains against known ones based on their similarity. By integrating these technologies together, this new approach makes searching faster, precise, and consistency across many generations of life without losing any significant amount of knowledge about them.

Problems solved by technology

This patented technical problem addressed in this patents relates to identifying specific bacteria called genera within an organism's gastrointestinal tract through metallurgynthesis techniques such as metagronomycesceae growth. Current approaches involve collecting representative biosamples from each individual patient before testing them downstream because they require multiple steps like culturing their own cells and studying how those cellular components change over time. Additionally, previous studies focused mainly on single nucleation events rather than comprehensive datasets containing thousands of yeast metabonomese sequences.

Method used

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  • Construction method and system of microbial gene database
  • Construction method and system of microbial gene database
  • Construction method and system of microbial gene database

Examples

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Embodiment 1

[0078] Embodiment 1 microbial gene database construction system

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

[0080] The genome data acquisition 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, N≥1;

[0081] The gene prediction module is connected with the genome data acquisition storage module, and is used to perform gene prediction on the genome data obtained in the genome data acquisition module, and obtain and output the gene annotation file containing the sequence and annotation;

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

Embodiment 2

[0086] The microbial gene database construction system of embodiment 2 upgrade

[0087] This embodiment upgrades the construction system #1 of Example 1 to obtain the construction system #2. The improvement point is to further include 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-redundant the retained genes, extract single-copy comparison genes, and obtain non-redundant microbial gene databases.

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

[0089] For each species, de-redundancy is performed separately: filter all genes of the sequence class whose gene number is greater than 1, and all remaining genes are the only compared single-copy genes of this species;

[0090] Merge the deredundant genes of all species, and filter all genes of the sequence class whose gene number is grea...

Embodiment 3

[0091] The microbial gene database construction system of embodiment 3 upgrade

[0092] This example upgrades the construction system #1 of Example 1 or the construction system #2 of Example 2 to obtain construction system #3 and construction system #4. The improvement points are: in the representative genome analysis module and the gene comparison module Among them, a gene filter module is further included, which is respectively connected with the representative gene acquisition module and the gene comparison module, and is used to receive and filter the representative genes output by the representative gene acquisition module: filter the genes whose sequence length is less than 200, and then filter the Representative genes are exported to the gene comparison module.

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Abstract

The invention discloses a construction method and system of a microbial gene database, and belongs to the technical field of gene database construction. The method comprises the following steps: acquiring target microbial genome data, and performing gene prediction on the acquired genome data to obtain a gene annotation file containing sequence and species annotations; obtaining a representative gene of each target microorganism; respectively comparing each gene in the representative genes to a nucleic acid sequence database to obtain a comparison result; and filtering a comparison result to obtain gene annotation species information, and reserving genes of annotation species which are the same as the source species, so as to construct the microbial gene database. The microorganism gene database constructed by the construction method can be updated according to the change of the target microorganism, the real-time performance is higher, and the microorganism database constructed by the method only contains the gene sequence of the target microorganism, so that the comparison time is shorter.

Description

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Claims

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Application Information

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Owner SHENZHEN AIMIGENE TECH CO LTD
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