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Method for data analysis of miRNA in plants with reference data based on miRBase database

A technology of data analysis and database, applied in the field of data analysis of plant miRNA sequencing

Active Publication Date: 2019-07-16
南京派森诺基因科技有限公司
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  • Abstract
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  • Application Information

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Problems solved by technology

At present, there is no ready-made process to analyze plant small RNA sequencing data; especially there is no automated analysis platform to realize the process analysis tools of plant small RNA sequencing results, including subsequent sRNA annotation, miRNA sequence feature analysis, expression analysis and differential analysis , target gene locus analysis, and other automated integration steps

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  • Method for data analysis of miRNA in plants with reference data based on miRBase database
  • Method for data analysis of miRNA in plants with reference data based on miRBase database
  • Method for data analysis of miRNA in plants with reference data based on miRBase database

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Embodiment Construction

[0047] The present invention will be further described by the following examples, but these examples should not be used to explain the limitation of the present invention.

[0048] In step S1), the user's small RNA sequencing data and related database information are accepted, and then all data are analyzed to obtain annotation information of all small RNAs in each sample, and sequence characteristics analysis and expression of miRNAs are performed Quantitative analysis, as well as differential expression analysis between samples, function and pathway enrichment analysis.

[0049] The first is to filter and count the disembarkation data. In the embodiment of the present invention, the off-machine data is filtered to remove adapters and low-quality sequences, so as to obtain high-quality sequencing results. As an example, the perl language script is used to remove the linker sequence (filter_data.py script), and the original sequence is searched through a 5bp sliding window. W...

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Abstract

The invention discloses a method for data analysis of miRNA in plants with reference data based on a miRBase database. The method is characterized by comprising the following steps of filtration of logout data, sRNA classification and annotation, miRNA differential analysis, miRNA function and pathway analyses, miRNA sequence feature analysis, and result sorting. The method disclosed by the invention has the beneficial effects that the proper analysis method is adopted aiming at the features of the miRNA of the plants; a result is comprehensive and comprises involved miRNA analysis content andother detected small RNA information annotation; all analysis results are automatically sorted; after analysis of each part is completed, automatic statistics of the results is achieved, and the results are visualized, classified and sorted, so that result arrangement is clear and is directly used for report generation; all operation steps are visible, and errors can be conveniently queried.

Description

technical field [0001] The invention relates to the field of transcriptome sequencing, in particular to a data analysis method for plant miRNA sequencing with reference data in a miRBase database. Background technique [0002] miRNA is a class of non-coding single-stranded RNA molecules encoded by endogenous genes, which participate in post-transcriptional gene expression regulation in animals and plants. Most miRNAs exist in the genome in the form of single copy, multiple copies or gene clusters. miRNAs are widely found in many species and are highly conserved in the evolutionary process. Therefore, studying the exact function of miRNAs, target genes, and their mechanisms of action is an important part of transcriptomics data analysis, which is crucial for understanding genes in organisms. The mechanism of expression regulation is of great significance. [0003] There are obvious differences in the mechanism of action of miRNA between animals and plants, and some species ...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B25/10G16B30/00G16B45/00
CPCY02A90/10
Inventor 王玲平王智健姜丽荣沈立孙子奎
Owner 南京派森诺基因科技有限公司
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