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A miRNA prediction method, a miRNA system and applications

A prediction method and seed technology, applied in the direction of biochemical equipment and methods, microbial determination/inspection, etc., can solve the problems of long running time, increase the consumption of computing resources, affect the project cycle, etc., and achieve high efficiency.

Inactive Publication Date: 2019-01-29
BGI TECH SOLUTIONS
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  • Description
  • Claims
  • Application Information

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Problems solved by technology

These miRNA prediction methods are all based on single sequencing results. Parallel analysis of data from different batches or different laboratories needs to be carried out together, which not only affects the project cycle, but also increases the consumption of computing resources; and, the existing The overall running time of the miRNA prediction method is long

Method used

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  • A miRNA prediction method, a miRNA system and applications

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Embodiment

[0042] In this example, the precursors of 20 human miRNAs are linked together with N as the simulated genome sequence, and miRNA prediction is performed on it. The simulated genome sequence obtained by splicing is the sequence shown in Seq ID No.1, and its length is 2566bp.

[0043] Seq ID No.1:

[0044] TGGGATGAGGTAGTAGGTTGTATAGTTTTAGGGTCACACCCACCACTGGGAGATAACTATACAATCTACTGTCTTTCCTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGTTGAGGTAGTAGGTTGTATAGTTTAGAATTACATCAAGGGAGATAACTGTACAGCCTCCTAGCTTTCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGGGGTGAGGTAGTAGGTTGTGTGGTTTCAGGGCAGTGATGTTGCCCCTCGGAAGATAACTATACAACCTACTGCCTTCCCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCATCCGGGTTGAGGTAGTAGGTTGTATGGTTTAGAGTTACACCCTGGGAGTTAACTGTACAACCTTCTAGCTTTCCTTGGAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTAGGAAGAGGTAGTAGGTTGCATAGTTTTAGGGCAGGGATTTTGCCCACAAGGAGGTAACTATACGACCTGCTGCCTTTCTTAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCGGGCTGAGGTAGGAGGTTGTATAGTTGA...

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Abstract

The invention discloses a miRNA prediction method, a miRNA system and applications. The miRNA prediction method of the invention includes the following steps: (1) setting a length of a seed sequence;(2) fully arranging four bases A, T, C and G according to the set length to form a seed sequence set; (3) removing redundant sequences in the seed sequence set; (4) searching positions of the seed sequences on a genome to obtain a position set; (5) arranging the seed sequence position set from small to large; (6) traversing the positions of the position set, and if the sequences of the front and back positions complement each other and the distance is not greater than the length of the set precursor sequence, outputting the sequence; and (7) using secondary structure prediction software to perform secondary structure prediction on the output sequence to obtain miRNA, and generating a miRNA set of the species. The miRNA prediction method of the invention directly searches for the miRNA in the genome sequences, and so the obtained miRNA set is more complete. Furthermore, the miRNA prediction method is high in efficiency and more convenient, and lays the foundation for subsequent miRNA research.

Description

technical field [0001] The present application relates to the field of nucleic acid analysis and detection, in particular to a miRNA prediction method, a miRNA system obtained by the miRNA prediction method, and the application of the miRNA prediction method. Background technique [0002] miRNA is a kind of non-coding single-stranded RNA molecule encoded by endogenous genes with a length of about 22 nucleotides. It regulates gene expression through complete or incomplete complementary combination with genes, thereby causing differences in shape and phenotype. At present, there are many miRNA-related databases, such as miRBase, Tarbase, etc., which are conducive to downstream analysis of miRNA. However, except for a small number of model organisms, the number of known miRNAs in most species is very limited. For example, only 173 miRNAs are included in miRBase for amphioxus, which limits further research on miRNAs to some extent. Therefore, for The identification of potential...

Claims

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Application Information

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IPC IPC(8): C12Q1/6869
CPCC12Q1/6888C12Q2600/178
Inventor 朱欠华黎万顺万胜青
Owner BGI TECH SOLUTIONS
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