Transcription factor binding site prediction method fusing with DNA shape features

A shape feature and binding site technology, applied in the field of bioinformatics, can solve problems such as good prediction of TF binding preference, and achieve the effects of strong usability, low design complexity, and short training time

Active Publication Date: 2021-11-02
OCEAN UNIV OF CHINA
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Problems solved by technology

Although an improvement over similar models that only consider motif information, this approach was trained and validated using only normalized DNase-seq data from 15 cell types and information on 5 specific core histone modifications, which m

Method used

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  • Transcription factor binding site prediction method fusing with DNA shape features
  • Transcription factor binding site prediction method fusing with DNA shape features
  • Transcription factor binding site prediction method fusing with DNA shape features

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Embodiment 1

[0028] Step A fusion DNA specific shape features transcription factor binding site prediction, the method bits are as follows:

[0029] Construction 1, the data set

[0030] First, in-depth study of the underlying mechanisms related to scientific progress -DNA binding proteins, as well as summarize the current status and recent development of DNA transcription factor binding site prediction, collect survey data sets mainstream sources of information in the field. Secondly, the fusion DNA shape characteristics and sequence information transcription factor binding site prediction model, in-depth study DNA shape characteristics acquired relevant developments methods, as well as DNA transcription factor binding site prediction related data set construction method, designed and constructed with DNA shape specific characteristic data and the data set of DNA sequence information.

[0031]Method using HT-MC DNA shape characteristics acquired, previous studies to improve efficiency by redu...

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Abstract

The invention relates to a transcription factor binding site prediction method fusing DNA shape features, belongs to the field of bioinformatics, and provides a new model for predicting transcription factor binding sites by using CNN in combination with DNA sequence and shape feature information by combining knowledge of structural biology, genomics and a deep learning neural network. Meanwhile, a special data set containing DNA shape features and DNA sequence information is constructed, and corresponding DNA shape information is added on the basis of a traditional transcription factor prediction data set. Therefore, the prediction accuracy of the DNA transcription factor binding site is improved.

Description

Technical field [0001] The present invention is in the field of bioinformatics, structural biology and combined knowledge of genomics design and implement a new method wherein a shape of the fusion DNA transcription factor binding site prediction. Background technique [0002] Transcription factor (TF) expression of many genes may be coordinated by binding to regulate transcription of the genomic region. With these primary cellular mechanism to regulate critical regulator of cellular processes and adapt to environmental stimuli. In fact, TF sequence or the number of changes may be hereditary diseases, complex diseases, autoimmune deficiencies and the main reason for cancer. How TF regulatory sequence specific DNA (referred to as TF binding sites, or simply of TFBS, such as promoters, enhancers) binding to coordinately regulated gene transcription and protein synthesis is a very important process, which in many biological processes from a key role. Over the past decade, have gener...

Claims

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Application Information

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IPC IPC(8): G16B15/30G16B20/30G06N3/04G06N3/06G06N3/08
CPCG16B15/30G16B20/30G06N3/061G06N3/084G06N3/045
Inventor 李阳阳魏志强刘昊闫金盟
Owner OCEAN UNIV OF CHINA
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