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Method for predicting interaction between sRNA and target mRNA of sRNA in bacteria

A prediction method and target technology, applied in instrumentation, genomics, proteomics, etc., can solve problems such as dependence

Active Publication Date: 2019-06-07
GUILIN UNIV OF ELECTRONIC TECH
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Problems solved by technology

Such approaches have contributed greatly to identifying whether sRNAs and their target mRNAs interact, but they rely on more biochemical experimental data to characterize

Method used

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  • Method for predicting interaction between sRNA and target mRNA of sRNA in bacteria
  • Method for predicting interaction between sRNA and target mRNA of sRNA in bacteria
  • Method for predicting interaction between sRNA and target mRNA of sRNA in bacteria

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Embodiment

[0049] refer to figure 1 , a method for predicting the interaction between sRNA and its target mRNA in bacteria, comprising the steps of:

[0050] 1) Data collection and arrangement: Obtain the sRNA-mRNA interaction data set from the sRNATarBase 3.0 database, compare the mRNA primary sequence in the data set with the corresponding mRNA whole genome sequence in the NCBI database, and intercept the mRNA upstream of the start codon The sequence fragment between 80nt and downstream 50nt, the start codon is AUG, and then, connect the sRNA sequence and the mRNA sequence to form a sequence pair, each sequence pair is composed of one sRNA sequence and one mRNA sequence, such as: sRNA -LLLLLL-mRNA, where L is the connection symbol, and the curated data set includes 241 positive sample RNA sequence pairs with interactions and 185 negative sample RNA sequence pairs without interaction;

[0051] 2) feature extraction, data set is converted into matrix: its process is:

[0052] Suppose t...

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Abstract

The invention discloses a method for predicting interaction between sRNA (small RNA) and target mRNA (messenger RNA) of sRNA in bacteria. The method includes the steps: 1) data collection and sorting;2) feature extraction, conversion of a data set into a matrix; 3) F-score feature optimization; and 4) training and construction of an SVM model, prediction and obtaining of a prediction result. Themethod for predicting interaction between sRNA and target mRNA of sRNA in bacteria can effectively characterize RNA sequence information and improve the prediction accuracy of sRNA-target mRNA interaction. At the same time, the method for predicting interaction between sRNA and target mRNA of sRNA in bacteria has the advantages of low cost, low time consumption and high prediction speed.

Description

technical field [0001] The invention relates to classification prediction of sequence interaction in bioinformatics, in particular to a prediction method of interaction between sRNA and its target mRNA in bacteria. Background technique [0002] Non-coding RNA (non-coding RNA, referred to as ncRNA) is a kind of RNA that does not code for protein. Since ncRNAs with certain regulatory functions were identified in rapid succession, ncRNAs have attracted more and more attention in molecular biology. . Regulation of the interaction between ncRNA and messenger RNA (messenger RNA, mRNA for short) inhibits or activates the translation into protein, resulting in the regulation disorder of gene expression, which leads to the occurrence of diseases. In this kind of regulation, the more popular ones include small RNA (small RNA, sRNA for short) in bacteria, which forms a complex secondary structure with the target mRNA through base pairing, directly or indirectly affecting the genes in ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B40/00G16B20/00G16B30/10
CPCY02A90/10
Inventor 樊永显崔娟张龙张向文
Owner GUILIN UNIV OF ELECTRONIC TECH
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