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Method for quickly predicting target gene of target miRNA

A target gene and target technology, which is applied in the field of rapid prediction of the target gene of target miRNA, can solve the problems of large memory consumption and long running cycle, and achieve the effect of reducing memory consumption, shortening running time, and significant application value

Active Publication Date: 2019-08-23
BGI TECH SOLUTIONS
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, these software need to traverse miRNA and all target genes, and the running cycle is long, and during the prediction process, all target gene sequences need to be loaded into memory, which consumes a lot of memory, especially some target gene sequences are relatively large species

Method used

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  • Method for quickly predicting target gene of target miRNA
  • Method for quickly predicting target gene of target miRNA

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Experimental program
Comparison scheme
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Embodiment 1

[0047] Embodiment 1, establish the method for predicting the target gene of target miRNA

[0048] The inventors of the present invention have established a method for predicting target genes of target miRNAs through a large number of experiments. Specific steps are as follows:

[0049]1. Obtain 31224 human reference genome hg19 sequences from UCSC (URL: http: / / genome.ucsc.edu).

[0050] 2. Perform k-mer segmentation on the sequence of the human reference genome hg19 obtained in step 1 (the length of k-mer is set to 5), and obtain 1137 kinds of k-mers (because there are some special features at the front of the sequence of the human reference genome hg19). Purine or pyrimidine (non-ATCG), so the number of k-mer types exceeds 1024 (4 5 )kind).

[0051] 3. After completing step 2, store the data of each k-mer and the corresponding position in the computer to obtain the BDMT file.

[0052] Among them, the k-mer is stored in capital letters, and the corresponding position is st...

Embodiment 2

[0065] Embodiment 2, the comparison of the method established in embodiment 1 and the software of the target gene of existing prediction target miRNA

[0066] In this example, the names of the 21 target miRNAs are listed in column 1 in Table 1, and their corresponding nucleotide sequences are listed in column 2 in Table 1.

[0067] 1. Using RNAhybrid software to predict the target genes of 21 target miRNAs

[0068] Use RNAhybrid software (recorded in the following literature: Rehmsmeier, Marc and Krueger, JanRNAhybrid: microRNA target prediction easy, fast and flexible, Nucleic AcidsRes., 2006) to predict the target genes of 21 target miRNAs respectively. The running parameters are: -b 100 -c -f 2,8 -m100000 -v3 -u 3 -e -20 -p 1 -s 3utr_human.

[0069] The number of target genes of each target miRNA predicted by RNAhybrid software is shown in the third column in Table 1.

[0070] Table 1

[0071]

[0072]

[0073] 2. Using miRanda software to predict the target genes ...

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Abstract

The invention discloses a method for quickly predicting a target gene of a target miRNA. The method comprises the following steps of (1), segmenting the sequence of a species genome by k-mer, and obtaining a first k-mer combination; segmenting a target miRNA by the k-mer and obtaining a second k-mer combination; (2), storing each k-mer in the first k-mer combination and the corresponding target gene information, and obtaining a database; and (3), retrieving the reverse complementary sequence of each k-mer in the second k-mer combination in the database, and predicting the target gene of the target miRNA according to a retrieving result. The target genes of 21 target miRNAs are predicted by means of RNAhybrid software, miRanda software and the method of the invention. A result proves a factthat the method according to the invention can predict the target gene of the target miRNA and greatly reduces operation time. The method has high application value.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular to a method for quickly predicting target genes of target miRNAs. Background technique [0002] miRNA is a non-coding short-chain RNA with a length of about 21-23nt. It participates in a series of important processes in life activities by regulating target genes, such as early development, cell proliferation, cell apoptosis, cell differentiation and other biological functions. With the development of bioinformatics and the improvement of cloning technology, about 320 miRNAs have been found in humans, which is about 1% of coding genes. The complementary relationship between miRNA and target genes is the basis for studying miRNA regulation. Different complementary binding modes between miRNA and target genes may produce different regulatory results. Generally speaking, miRNA is fully complementary to the target gene, and its mode of action and function are very similar to siRNA, which ...

Claims

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Application Information

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IPC IPC(8): G16B25/00
CPCG16B25/00
Inventor 朱欠华杨林峰黎万顺万胜青
Owner BGI TECH SOLUTIONS