miRNA (micro Ribonucleic Acid) forecasting method

A prediction method and technology of prediction model, applied in the field of miRNA prediction, can solve the problems of miRNA lack of evolutionary conservation and unsuitability, and achieve the effect of ensuring internal and external prediction ability, easy operation and efficient prediction

Inactive Publication Date: 2010-09-29
CHONGQING UNIV
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Problems solved by technology

However, for some miRNAs, such as those cloned from virus-infected cells, there is hardly any evolutionary conservation
Therefore, the above prediction algorithm is not suitable for the prediction of this type of miRNA

Method used

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  • miRNA (micro Ribonucleic Acid) forecasting method

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Embodiment Construction

[0013] The following will use the method of the present invention for human gene miRNA prediction as an example to describe in detail, including the following steps:

[0014] a) Select 514 two-dimensional property parameters of 5 kinds of bases (A, C, G, T and U), including molecular electric distance vector (MEDV), molecular holographic distance vector (MHDV), topology, operation and number of paths , connectivity index, information index, autocorrelation, edge adjacency index, Burden eigenvalue, topological charge index and eigenvalue index.

[0015] Principal component analysis is used to process 514 kinds of property parameters, and 4 principal components are obtained, which accumulatively explain 99.80% of the variance of the original data matrix (5×514). The scores of each principal component are shown in Table 1. Therefore, these 4 principal component score matrices (5×4) instead of the original variable matrix (5×514). For convenience, these four principal component s...

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Abstract

The invention discloses an miRNA forecasting method, which is characterized by comprising the following steps: (a) according to a principal component analysis method, establishing a new nucleotide sequence structure characterization method to obtain base two-dimensional characteristic scores; (b) characterizing the structures of the miRNAs and the non-miRNAs of human genes by the base two-dimensional characteristic scores; (c) carrying out normalization processing on the characterization variables of each miRNA and each non-miRNA by using a self-cross covariance method; (d) selecting parameters closely related with the miRNA structural characteristics by using a step-by-step method and establishing an miRNA forecasting model by a linear discriminatory analysis method; and (e) verifying the forecasting ability of the forecasting method by respectively adopting self-substitute verification, 1/5 reserving method cross verification and external verification. The miRNA forecasting method can be used for miRNA forecasting to discover new unknown miRNA genes.

Description

technical field [0001] The invention relates to a gene prediction method, in particular to a miRNA prediction method. Background technique [0002] miRNAs have a wide range of functions in organisms, and they mainly realize their regulatory functions through complementary pairing with target sequences. Due to the important regulatory role of miRNA in organisms, people are trying to find miRNAs in various organisms by various methods. Recent findings have shown that there are many more miRNAs than are known, and finding new miRNAs experimentally has become increasingly difficult. With the continuous enrichment of miRNA corresponding data, the use of bioinformatics methods to predict miRNA has been more and more widely used. At present, most miRNA prediction methods are mainly based on the conservation of miRNA in the evolution process, such as MiRscan software (Lim et al., Genes & Development, 2003, 17: 991) and miRSeeker software (Lai et al., Genome Biol, 2003, 4: R42) et...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68G06F19/00
Inventor 梁桂兆赵巍马秀岩杨力
Owner CHONGQING UNIV
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