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Method for predicting DNA transcription terminator in bacterium

A technology of transcription terminator and prediction method, applied in the field of DNA transcription terminator prediction in bacteria, which can solve problems such as accuracy

Active Publication Date: 2019-10-25
GUILIN UNIV OF ELECTRONIC TECH
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  • Description
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  • Application Information

AI Technical Summary

Problems solved by technology

[0005] The present invention provides a method for predicting DNA transcription terminators in bacteria to solve the problem of the accuracy of the existing terminator predictions

Method used

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  • Method for predicting DNA transcription terminator in bacterium
  • Method for predicting DNA transcription terminator in bacterium
  • Method for predicting DNA transcription terminator in bacterium

Examples

Experimental program
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Embodiment

[0079] In this example, in order to clearly represent the extracted multiple feature sets, the feature sets are numbered. The numbers in each table are the feature set categories, and Sn, Sp, Mcc, and Acc are also used as the evaluation methods in the table. , where Sn represents the model sensitivity, Sp represents the model specificity, Mcc represents the Matthews index of the model, and Acc represents the model prediction accuracy.

[0080] refer to figure 1 , a method for predicting DNA transcription terminators in bacteria, comprising the steps of:

[0081] 1) Obtain bacterial terminator and non-terminator sequences as benchmark data sets and independent data sets: In this example, 4 data sets are obtained from http: / / lin-group.cn / server / iTerm-PseKNC / website, such as figure 2 , image 3 As shown, that is, 280 E. coli terminator sequences, 560 E. coli non-terminator sequences, 425 Bacillus subtilis terminator sequences and 147 E. coli terminator sequences, of which 280...

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Abstract

The invention discloses a method for predicting a DNA transcription terminator in a bacterium. The method comprises the following steps of 1), acquiring a terminator and a non-terminator sequence of the bacterium as a reference data set and an independent data set; 2), performing characteristic set extraction; 3), performing characteristic set sequencing; 4), performing characteristic set selection; 5), performing characteristic set extraction method comparison; 6), training a model; 7), constructing a combined classifier; and 8), performing method evaluation. The predicting method has advantages of extracting the characteristic in various kinds of DNA information, reducing calculation time, preventing overfitting, selecting an optimal classifying model and improving accuracy in predictingthe terminator.

Description

technical field [0001] The invention relates to a classification prediction technology of sequence interaction in bioinformatics, in particular to a prediction method of DNA transcription terminator in bacteria. 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 basis of a large amount of i...

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Application Information

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IPC IPC(8): G16B40/00G16B30/10
CPCG16B40/00G16B30/10
Inventor 樊永显王婉茹朱庆琪徐海波崔娟
Owner GUILIN UNIV OF ELECTRONIC TECH