Method for identifying DNA promoter element based on information theory

A promoter and information theory technology, applied in the field of identifying DNA promoter elements based on information theory, can solve the problems of time-consuming and material-consuming, and achieve good prediction performance and high prediction accuracy

Pending Publication Date: 2021-10-15
TIANJIN UNIV
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Problems solved by technology

However, computational biology is gradually becoming a more favored classification method due to the time-consuming and expensive nature of performing biological experiments

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  • Method for identifying DNA promoter element based on information theory
  • Method for identifying DNA promoter element based on information theory
  • Method for identifying DNA promoter element based on information theory

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Embodiment Construction

[0042] Promoter determines the initiation of DNA sequence-specific transcription and is an important regulatory element necessary for gene expression. Identifying and locating promoters is helpful for the accurate positioning of genes, and will play an important guiding role in annotating the structure and function information of biological genomes. In the process of gene transcription, when RNA polymerase specifically binds to a specific promoter, it needs a specific σ protein factor to assist in the recognition. Therefore, the σ factor is often used to mark the type of promoter, which is recorded as σ 24 , σ 28 , σ 32 , σ 38 , σ 54 , σ 70 . At present, the traditional biological experimental methods used to identify promoters and their types are time-consuming, laborious and costly. In contrast, using bioinformatics algorithms to identify and classify is a more economical and convenient method.

[0043] The basic idea of ​​the invention is to extract the position-speci...

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Abstract

The invention discloses a method for identifying a DNA promoter element based on an information theory, the method is based on a double-layer identification model for judging different types of promoters, and the double-layer identification model carries out promoter sequence identification through the following steps: step 101: obtaining a promoter sequence data set through an escherichia coli database; step 102, performing position specific frequency extraction of trinucleotide composition information and dinucleotide composition information on the DNA promoter sequence data through a PSTNP algorithm; and step 103, optimizing the position specific frequency information of the trinucleotide composition information and the dinucleotide composition information. The promoter element type identification layer performs resampling processing on data sets of different promoter types by using an SMOTE algorithm; the prediction problem of a DNA promoter and the specific type of the DNA promoter is solved, feature optimization is performed on the extracted sequence frequency information by adopting an information theory method, and the prediction precision is obviously improved.

Description

technical field [0001] The invention belongs to the field of functional element prediction algorithms in bioinformatics, in particular to a method for identifying DNA promoter elements based on information theory. Background technique [0002] A promoter is a DNA regulatory element located near the transcription start site upstream of a gene, which controls the initiation of gene-specific transcription and determines the time and level of gene expression. Accurate positioning of promoters can achieve accurate positioning of genes. Therefore, identifying promoters is of great significance for studying gene structure and annotating gene information at the genome level. When the promoter specifically binds to RNA polymerase, it can be recognized by σ factors with different functions and structures, so the promoters are divided into σ 24 , σ 28 , σ 32 , σ 38 , σ 54 and σ 70 Six types. Currently, researchers are still primarily identifying these promoters through biologica...

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Application Information

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IPC IPC(8): G16B30/00G06F17/16G06K9/62
CPCG16B30/00G06F17/16G06F18/2411
Inventor 郭菲吕一诺何文颖唐继军曹晶
Owner TIANJIN UNIV
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