Xgboost-based whole-genome RNA secondary structure prediction method

Abstract

The invention provides an Xgboost-based whole-genome RNA secondary structure prediction method. The method includes the following steps that: an RNA sequence and the probability values of the pairingof base sites in the RNA sequence are obtained; a base with a high probability of pairing, and bases of a certain length at the upstream and downstream of the bases with the high probability are combined to form sequence fragments, and the sequence fragments are adopted as positive samples; a base with a low probability of pairing, and bases of a certain length at the upstream and downstream of the bases with the low probability are combined to form sequence fragments, and the sequence fragments are adopted as negative samples; the positive samples and the negative samples are combined into sample data sets, and the sample data sets are divided into a training set and a test set, and the training set and the test set are loaded into a machine learning model established based on the Xgboostalgorithm, and the machine learning model is trained and tested; and the trained and tested machine learning model is used to predict an RNA secondary structure. With the method adopted, when the RNAforms the secondary structure, the probability scores of the paring of each base site are obtained; and with the probability scores adopted, a judgment basis can be provided for the formation of thesecondary structure in the next step.

Description

technical field [0001] The invention relates to the field of bioinformatics research, in particular to an Xgboost-based method for predicting the secondary structure of whole-genome RNA. Background technique [0002] The prediction of RNA secondary structure is an important research field of molecular biology, and it is of great significance to promote the development of life science. The molecular structure of RNA consists of three levels: primary structure, secondary structure, and tertiary structure. The RNA secondary structure refers to the stem-loop structure formed by the RNA sequence itself. It is a structure between the primary structure and the tertiary structure, and stores more high-level structural information. Therefore, the study of the RNA secondary structure has become a Important research questions in the field of bioinformatics. There are mainly two methods to determine the secondary structure: the experimental method of physical chemistry and the predict...

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But in fact, artificial threshold setting often leads to the problem of too many or too few output targets, which greatly affects the accuracy rate, etc.

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