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A Prediction Method of DNA Replication Origin in Saccharomyces cerevisiae

A technology of Saccharomyces cerevisiae and origin of replication, applied in neural learning methods, sequence analysis, instruments, etc., to achieve the effects of reducing calculation time, improving accuracy, and avoiding overfitting

Active Publication Date: 2022-05-17
GUILIN UNIV OF ELECTRONIC TECH
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Problems solved by technology

[0005] The object of the present invention is to solve the problem of the accuracy rate of the prediction of the existing DNA replication origin, and provide a kind of prediction method of the DNA replication origin in Saccharomyces cerevisiae, this prediction method can extract the feature in various DNA information, also reduces calculation time, to avoid over-fitting, and to construct an optimal classification model to improve the accuracy of predicting the origin of replication

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  • A Prediction Method of DNA Replication Origin in Saccharomyces cerevisiae
  • A Prediction Method of DNA Replication Origin in Saccharomyces cerevisiae
  • A Prediction Method of DNA Replication Origin in Saccharomyces cerevisiae

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Embodiment

[0045] Such as figure 1 Shown, a kind of prediction method of DNA replication origin in Saccharomyces cerevisiae, comprises the steps:

[0046] 1) Obtaining sample data sets: 405 positive sample sequences containing replication origins and 406 negative sample sequences not containing replication origins in Saccharomyces cerevisiae were collected, such as figure 2 shown;

[0047] 2) Feature extraction: use the binary coding method and PSEKNC-I to represent the sample sequence, that is, use a vector to represent each NDA sequence;

[0048] The binary encoding method uses 0 and 1 to represent the nucleotides in the DNA sequence, and converts each DNA sequence into a feature vector. The representation of the nucleotides in the DNA sequence is as follows:

[0049]

[0050] In formula (1), A(0,0,0,0) is adenine in DNA sequence, C(0,1,0,1) is cytosine in DNA sequence, G(0,0,1, 0) is guanine in the DNA sequence, and T(0,0,0,1) is thymine in the DNA sequence.

[0051] PSEKNC-I ...

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Abstract

The invention discloses a method for predicting the origin of DNA replication in Saccharomyces cerevisiae. The steps are: obtaining positive sample sequences and negative sample sequences in Saccharomyces cerevisiae; using two methods of binary coding and PSEKNC‑I to extract features; using F The ‑score and IFS methods screen the features obtained by the PSEKNC‑I method to obtain pre-screened features; combine the features obtained by the binary coding method with the pre-screened features to obtain a sample data set after feature combination; construct and train a CNN prediction model, Input data to obtain preliminary prediction results; adjust the parameters in the trained CNN prediction model to optimize the trained CNN prediction model; use the five-fold cross-validation method to evaluate the optimized CNN prediction model and finally obtain the optimal CNN prediction model. Input the data into the optimal model to get the final prediction result. The method extracts features from various DNA information, reduces calculation time, avoids over-fitting phenomenon, selects the optimal classification model, and improves the accuracy of predicting the origin of replication.

Description

technical field [0001] The invention relates to the technical field of classification and prediction of sequence interactions in bioinformatics, in particular to a method for predicting DNA replication origins in Saccharomyces cerevisiae. Background technique [0002] In recent years, a new research direction has been derived from the combination of bioinformatics and computer science, which takes nucleotide, protein, and gene sequence data sets as the main research objects, and uses mathematics, informatics, and computer science to Computer hardware, software, and computer network are the main tools to store, manage, annotate, and process an extremely large amount of raw data, making it biological information with clear biological meaning. And through the query, exploration, comparison and analysis of biological information, rational knowledge such as gene coding, gene regulation, nucleotide and protein structure, function and machine relationship can be obtained. On the b...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B40/00G16B30/00G06K9/62G06N3/04G06N3/08
CPCG16B40/00G16B30/00G06N3/08G06N3/045G06F18/2113
Inventor 樊永显王婉茹
Owner GUILIN UNIV OF ELECTRONIC TECH