Toxin gene abundance detection method based on metagenomics and annotation database construction method
A technology of metagenomics and detection methods, applied in biochemical equipment and methods, combinatorial chemistry, chemical library, etc., can solve problems such as inability to measure strength, achieve convenient transportation, and improve the effect of treatment
- Summary
- Abstract
- Description
- Claims
- Application Information
AI Technical Summary
Problems solved by technology
Method used
Image
Examples
Embodiment 1
[0038] see attached figure 1 , is a schematic flowchart of a metagenomics-based toxin gene abundance detection method provided in the embodiment of the present invention, the method may include the following steps:
[0039] S1. Sample collection and library building and sequencing to obtain metagenomic sequencing data of the sample to be tested.
[0040] In order to study the characteristics of intestinal endotoxin genes, 1005 volunteers were recruited, their stool samples were collected and quantitative metagenomic sequencing was performed. The amount of sequencing data for each sample was not lower than that of 5G sequencing data to obtain as many toxins as possible. genetic information.
[0041] In one implementation of the embodiment of the present invention, the fecal tissue of the user is collected and detected, the bacterial flora DNA in the fecal tissue is extracted and quality controlled, and a known amount of internal reference DNA is added to the bacterial flora DN...
Embodiment 2
[0060] Another aspect of the present invention provides a method for constructing and annotating a specific toxin factor annotation database,
[0061] Annotate the species origin and functional classification of each toxin gene sequence, integrate the annotation information into the toxin factor reference sequence database, and form the toxin factor annotation database, and then conduct KEGG annotation analysis on the toxin factor through the toxin factor annotation database, and the results are shown in the appendix figure 2 shown.
[0062] from figure 2 As can be seen in , genes for ubiquitous adhesion, antiphagocytic and secreted toxin factors were detected.
[0063] Based on the pre-established toxin factor annotation database, the detected toxin factors were further annotated, and the species associated with the toxin factors, the mechanism of action, etc. were explained. Some results of the final detection are shown in Table 1.
[0064] Table 1 Annotation results of ...
experiment example
[0067] data simulation
[0068] In order to study the performance of this method in detecting toxin genes, using the DNA sequences in the toxin factor reference sequence database, 10M simulated sequencing sequences were simulated using InSilicoSeq software, and the theoretical sequence number and relative abundance of each toxin gene were calculated.
[0069] Toxin gene abundance calculation
[0070] Using Bowtie2 to compare the simulated sequencing sequence to the reference sequence of the toxin gene, count the number of sequences on each toxin gene alignment, and use the RPKM method for further normalization to obtain the relative abundance of each toxin gene.
[0071] Algorithm performance analysis
[0072] In order to evaluate the accuracy and sensitivity of this calculation method, the theoretical relative abundance was compared with the real abundance, and the results are shown in the attached image 3 As shown, it can be seen from the figure that in the simulated data...
PUM
Login to View More Abstract
Description
Claims
Application Information
Login to View More