Method for identifying DNA enhancer element based on sequence frequency information

Abstract

The invention discloses a method for identifying a DNA enhancer based on sequence frequency information. The method is based on a double-layer DNA enhancer prediction model established by a support vector machine, and the prediction model is generated by the following steps: step (1): constructing a DNA enhancer sequence data set through chromatin database information of a cell line; step (2) processing the DNA enhancer sequence data set through a PSTNP algorithm to obtain DNA enhancer information of a trinucleotide sequence with position specificity; step (3), the trinucleotide sequence information of the DNA enhancer information being optimized through a Kullback-Leibler divergence algorithm; step (4) carrying out dimension reduction processing on the characteristic data of the trinucleotide sequence of the DNA enhancer information by adopting an LASSO algorithm. The prediction problem of the DNA enhancer and the strength of the DNA enhancer is solved, the extracted sequence frequency information is improved by adopting a feature optimization and feature screening 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 enhancer elements based on sequence frequency information. Background technique [0002] Transcription is the first and crucial step in gene expression, which is controlled by regulatory elements such as promoters and enhancers. Among them, enhancer is a short sequence (50-1500bp) on DNA, which has the ability to recruit transcription factors and their complexes, thus increasing the possibility of certain gene transcription. By predicting the enhancers in the DNA sequence, researchers in the biological field can help find the reasons for the abnormal increase in transcription levels, and enhancers of different strengths make it possible to program and regulate transcription levels. Therefore, the predictive classification of enhancers has important practical significance. However, because enhancers act in cis...

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Problems solved by technology

[0004] The present invention is characterized in that it solves the problem of identification of DNA enhancer element and its intensity prediction, and contains the following steps in turn:

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