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PEDV genome analysis method based on next-generation sequencing

A virus genome and analysis method technology, applied in the field of PEDV virus genome analysis based on next-generation sequencing, can solve problems such as inability to accurately identify the gene structure and affect PEDV virus genome splicing, and achieve the effect of avoiding omissions

Active Publication Date: 2020-05-26
SHANGHAI PASSION BIOTECHNOLOGY CO LTD
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Problems solved by technology

[0002] At present, the existing PEDV analysis methods have two limitations. First, there are some or even a large number of host pig genome sequences in the PEDV virus next-generation sequencing data, and the contamination of the host genome will affect the splicing of the PEDV virus genome.
Second, the method of splicing and predicting the gene structure of the virus is mainly based on prediction software such as GeneMarkS. However, due to the overlap of genes in the PDEV virus genome and the phenomenon of ribosomal frameshift inside the gene, the existing gene prediction software cannot accurately identify the correct gene. structure

Method used

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  • PEDV genome analysis method based on next-generation sequencing
  • PEDV genome analysis method based on next-generation sequencing
  • PEDV genome analysis method based on next-generation sequencing

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Experimental program
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Effect test

Embodiment 1

[0024] 1. The PEDV virus sample pedv1 was passed through the illumina Miseq sequencer to generate 2.4G of raw data, and 2.3G of high-quality sequences in fastq format were obtained after removing sequencing adapters and quality control.

[0025] 2. Since the host of the PEDV virus is a pig, download the reference genome and transcript sequence of the pig from the Ensembl website.

[0026] 3. Run bowtie2-build to build an index with the reference sequence downloaded in step (2) as input.

[0027] 4. Run the Bowtie2 software (default parameters) to compare the sequencing data with the host reference sequence in step (1).

[0028] 5. According to the comparison results, the data compared to the pig reference sequence were eliminated. Obtain sequence sequences free of host contamination.

[0029] 6. Since too much data volume is not conducive to splicing, the sequencing sequence without host contamination obtained in step (5) intercepts 4.2m of data volume about 150 times the si...

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Abstract

The invention discloses a PEDV genome analysis method based on next-generation sequencing. The method is characterized by comprising the following steps: downloading a genome sequence and a transcriptsequence of a host pig as a host reference sequence; acquiring a sequencing sequence for removing host pollution; splicing the genome; carrying out homologous comparison on the genome; selecting a comparison result; and taking the compared starting site as a starting site of the gene. Compared with the prior art, the method has the advantages that gene structure can be accurately predicted, and omission is avoided.

Description

technical field [0001] The invention relates to the field of gene detection, in particular to a method for analyzing the genome of PEDV virus based on next-generation sequencing. Background technique [0002] At present, the existing PEDV analysis methods have two limitations. First, there are some or even a large number of host pig genome sequences in the PEDV virus next-generation sequencing data, and the contamination of the host genome will affect the splicing of the PEDV virus genome. Second, the method of splicing and predicting the gene structure of the virus is mainly based on prediction software such as GeneMarkS. However, due to the overlap of genes in the PDEV virus genome and the phenomenon of ribosomal frameshift inside the gene, the existing gene prediction software cannot accurately identify the correct gene. structure. Contents of the invention [0003] In order to overcome the above-mentioned defects of the prior art, the object of the present invention i...

Claims

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Application Information

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IPC IPC(8): G16B20/00G16B30/00
CPCG16B20/00G16B30/00Y02A90/10
Inventor 崔天一孙子奎
Owner SHANGHAI PASSION BIOTECHNOLOGY CO LTD
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