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A feature analysis method for RNA editing sites

A technology of RNA editing and feature analysis, applied in the field of feature analysis of RNA editing sites, can solve the problems of energy investment, lack of analysis ideas, software and hardware support, etc.

Active Publication Date: 2016-04-27
BGI SHENZHEN CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Different from other DNA variations (such as snp, indel identification, etc.), the biological identification and analysis of RNA editing is still in its infancy. Therefore, there is a lack of unified analysis ideas and related software and hardware support, which has led to a lot of energy being invested repetitive work

Method used

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  • A feature analysis method for RNA editing sites
  • A feature analysis method for RNA editing sites
  • A feature analysis method for RNA editing sites

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0094] 1. Sample / data source

[0095] 1. In 165 prostate cancer patients, high-throughput sequencing was performed on the normal DNA, tumor DNA, normal RNA, and tumor RNA of each patient, with a read length of 90 bp, and the RNA editing site data and SNP site data of the population were analyzed and obtained to obtain RNA editing sites and corresponding annotation information in VCF format.

[0096] 1.2Darned database (URL: http: / / darned.ucc.ie / )

[0097] 2. Analysis and processing of RNA editing site data

[0098] In this embodiment, RNAfold software is used to analyze the characteristics of RNA editing sites. RNAfold software is open source software, and the download address is as follows: http: / / www.tbi.univie.ac.at / RNA / index.html#download .

[0099] For the convenience of description, the generated files and descriptions in this embodiment are listed in Table 1.

[0100] Table 1 Generated files and descriptions in this embodiment

[0101]

[0102]

[0103]

...

Embodiment 2

[0119] The steps in Example 1 were repeated, with the difference that the following samples were used to replace the 65 prostate cancer patients in Example 1, so as to obtain RNA editing site data sets and perform feature analysis:

[0120] Sample: 24 patients with lung cancer.

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Abstract

The invention provides a feature analysis method for RNA editing sites. The method comprises the steps of performing sequencing on to-be-analyzed samples and obtaining DNA and RNA data; analyzing the obtained data to obtain an RNA editing site data set; obtaining an RNA secondary structure free energy distribution curve of RNA editing site upstream and downstream sequences in the RNA editing site data set through statistics. The method can conveniently and rapidly analyze the basic features of RNA editing site data.

Description

technical field [0001] The invention belongs to the field of biotechnology, in particular, the invention relates to a method for analyzing the characteristics of RNA editing sites. Background technique [0002] RNA editing refers to the deletion, insertion or substitution of bases that occur at the RNA level after DNA transcription and before translation. In higher organisms, the most important RNA editing is the modification of base A to I (inosine), which is usually catalyzed by ADAR proteases. Since inosine nucleotide (I) is recognized as guanine nucleotide (G) at the translational level, this editing at this site is actually an A to G switch. This change may lead to changes in the structure and function of related proteins, and may also change the structure and function of RNA that plays a regulatory role in the organism. According to relevant literature reports, the phenomenon of RNA editing is closely related to the occurrence of cancer, so it has become a new resear...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/20G06F19/28
Inventor 李欣玥刘栋兵熊恒
Owner BGI SHENZHEN CO LTD
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