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A dna recombination site prediction method based on xgboost

A DNA recombination and prediction method technology, applied in the field of computational biology, can solve the problems of sequence limitation, low efficiency, time-consuming, etc., and achieve the effect of increasing recombination rate, improving prediction efficiency, and high visibility

Active Publication Date: 2022-05-27
SHANDONG JIANZHU UNIV
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Problems solved by technology

Its purpose is to solve the time-consuming and inefficient problems of current recombination site prediction experiments and the sequence limitation problem in the process of site recombination

Method used

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  • A dna recombination site prediction method based on xgboost
  • A dna recombination site prediction method based on xgboost
  • A dna recombination site prediction method based on xgboost

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Embodiment Construction

[0028] In order to clearly illustrate the technical solutions of the present invention, the following specific embodiments are combined with the appendix Figure 1-4 To illustrate the present invention, the examples herein are only used to explain the present invention, but not to limit the present invention.

[0029] It should be noted that the following detailed description is exemplary and intended to provide further explanation of the invention. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

[0030] figure 1 The workflow steps of XGBattCPred's method for predicting DNA recombination sites are shown. The DNA recombination site selected in this example is the attC site of the bacterial integration system, and the structural diagram of the attC site is as follows figure 2As shown, since the structure of this site is highly dependent ...

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Abstract

The present invention relates to the field of computational biology, and mainly relates to a method for predicting DNA recombination sites, in particular to a method for predicting DNA recombination sites based on XGBoost, including: preprocessing the data according to the samples of the initial data set , balance the positive and negative samples; construct the initial XGBoost regression prediction model; use the Optuna framework and the balanced data set to optimize the parameters of the model; train the optimized XGBoost regression prediction model; construct evaluation indicators to evaluate the performance of the model; according to the model For the reasonable judgment of the score, the model is processed until a stable high-precision model is obtained; finally, the recombination rate of the predicted site is output, and the feature is scored by the feature importance measure, and the feature score map is output. The invention has good portability and high prediction efficiency; it can discover unknown features that act on recombination, can effectively improve the design method of the synthesis site, and increase the recombination rate; it has high flexibility and scalability.

Description

technical field [0001] The invention relates to the field of computational biology, and mainly relates to a method for predicting a DNA recombination site, in particular to a method for predicting a DNA recombination site based on XGBoost. Background technique [0002] DNA recombination refers to the process of exchanging and recombining DNA fragments to form new DNA molecules by breaking and joining different DNA molecules. It is one of the basic tools used in genetic engineering. The development of DNA recombination technology has greatly promoted molecular biology. of rapid development. Site-specific recombination is a type of DNA recombination, which refers to the rearrangement of DNA sequences in the relative positions of DNA fragments. It does not depend on the homology of DNA sequences, but depends on the ability to combine with certain enzymes. the presence of DNA sequences. Studying the specific recombination sites of bacterial integrative subsystems can provide a...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/30G06K9/62G06F17/11
CPCG16B20/30G06F17/11G06F18/214G16B40/20G06F18/21
Inventor 刘振栋陈曦戴琼海李冬雁吕欣荣杨玉荣秦梦颖柏苛李晓峰季向阳刘烨斌张伟胡国胜刘芳含魏珑
Owner SHANDONG JIANZHU UNIV
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