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Method and system suitable for mixed-pool gene positioning

A technology of gene positioning and pooling, applied in genomics, instrumentation, proteomics, etc., can solve problems such as inability to perform parallel computing, slow speed, and low efficiency, so as to reduce randomness, ensure accuracy, and increase timeliness Effect

Pending Publication Date: 2019-11-12
SHANGHAI MAJORBIO BIO PHARM TECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0014] In the traditional BSA analysis method, the software used is the analysis software developed by R language, which runs on a single thread, with slow speed and low efficiency. Multiple methods can only be serialized and cannot be calculated in parallel.

Method used

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  • Method and system suitable for mixed-pool gene positioning
  • Method and system suitable for mixed-pool gene positioning
  • Method and system suitable for mixed-pool gene positioning

Examples

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no. 1 example

[0089] This example provides a method suitable for mixed pool gene location, such as figure 1 As shown, the execution process of the method includes three parts: mark filtering, statistical calculation, and result sorting; based on these three parts, the method of this embodiment is as figure 2 As shown, including the following steps:

[0090] S101, marking filtering, filtering molecular marking data based on preset marking quality information to obtain molecular marking data meeting the preset quality requirements;

[0091] S102, statistical calculation, performing statistical calculation on the molecular marker data obtained after filtering according to the group situation, to obtain statistical information;

[0092] S103. Sort the results, sort the obtained statistical information, and extract genetic information.

[0093] The above three parts are described further below:

[0094] 1. Mark the filtering part:

[0095] In order to ensure the accuracy of the analysis and the rationali...

no. 2 example

[0131] This embodiment provides a system suitable for location of mixed pool genes, and the system includes:

[0132] The label filter module is used to filter the molecular label data based on the preset label quality information to obtain the molecular label data that meets the preset quality requirements;

[0133] The statistical calculation module is used to perform statistical calculations on the molecular marker data obtained after filtering according to the group situation to obtain statistical information;

[0134] The result sorting module is used to sort the obtained statistical information and extract genetic information.

[0135] The system suitable for mixed pool gene localization in this embodiment corresponds to the method suitable for mixed pool gene localization in the above-mentioned first embodiment, wherein the functions implemented by each module in the system are the same as those applicable to mixed pool genes described above. Each process step in the positionin...

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Abstract

The invention discloses a method and system suitable for mixed-pool gene positioning. The method comprises the steps of mark filtering, wherein based on preset mark quality information, molecular markdata is filtered, and the molecular mark data meeting the preset quality demand is acquired; statistical calculation, wherein according to the population condition, the molecular mark data obtained after filtering is subjected to statistical calculation, and statistical information is acquired; result interpretation, wherein the acquired statistical information is subjected to interpretation, andgene information is extracted. Compared with a traditional BSA method, the scheme has the advantages that the application population range for positioning is enlarged, and F1, F2 and other populations can be positioned; by means of the scheme, a molecular mark is filtered in advance, residual redundant information is reduced, and the analysis efficiency is improved. In addition, compared with a traditional BSA single-thread analysis method, the method has the advantage that by using an HPC technology, the analysis speed is higher.

Description

Technical field [0001] The present invention relates to the technical field of gene positioning, in particular to a method and system suitable for mixed pool gene positioning. Background technique [0002] In gene mapping, BSA (Bulked Segregant Analysis) and genetic mapping are the most conventional and effective methods. The BSA analysis method was the first to screen out the markers linked to the target gene in lettuce. The method first selects a certain number of plants from any segregated population produced by a pair of parents with phenotypic differences of the target gene according to the phenotype of the target gene to form two subgroups or groups. The DNA of each group is mixed in equal amounts to form two "gene pools" of relative traits, and then the two gene pools are analyzed with appropriate molecular markers, and the molecular markers that show polymorphism between the two groups are inherited It is linked to the target trait gene locus. [0003] The traditional BS...

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Application Information

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IPC IPC(8): G16B20/20G16B50/30
CPCG16B20/20G16B50/30
Inventor 黄龙
Owner SHANGHAI MAJORBIO BIO PHARM TECH