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Automatic screening method, system and device for gene editing sites and storage medium

An automatic screening and gene editing technology, applied in the field of gene editing, can solve problems such as no change in gRNA protein expression, incomplete information sources, and unsatisfactory effects, and achieve automation, high cutting efficiency, and strong specificity

Pending Publication Date: 2021-04-06
广州源井生物科技有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

For beginners in gene editing, it takes a few days, and the effect is not necessarily ideal; for researchers with gene editing experience, they may not select gRNAs with higher cutting efficiency or selected knockouts because of incomplete information sources Protein expression remains unchanged after deletion of bases at the regional DNA level

Method used

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  • Automatic screening method, system and device for gene editing sites and storage medium
  • Automatic screening method, system and device for gene editing sites and storage medium
  • Automatic screening method, system and device for gene editing sites and storage medium

Examples

Experimental program
Comparison scheme
Effect test

Embodiment approach 1

[0094] Implementation Mode 1: Frameshift Knockout Scheme

[0095] (1) Determine the knockout region

[0096] S111. Determine whether the target gene is suitable for designing a knockout scheme. The specific method is as follows: obtain the position of the target gene on the chromosome from Ensembl, and search whether there are other genes in the segment where the target gene is located on the chromosome according to this position; if there are other genes, continue to obtain these genes that overlap with the target gene Types of other genes, if the other genes are protein-coding genes, then the target gene is not suitable for designing a knockout scheme.

[0097] S112. Preprocessing the transcript of the target gene. The specific method is: obtain the transcript information of the target gene from Ensembl, and exclude non-coding protein transcripts and incomplete transcripts.

[0098] S113. Find out the protein coding region of each transcript, that is, CDS. The specific m...

Embodiment approach 2

[0108] Embodiment 2: Small fragment knockout scheme

[0109] (1) Determine the knockout region

[0110] S121. Determine whether the target gene is suitable for designing a knockout scheme. The specific method is as follows: obtain the position of the target gene on the chromosome from Ensembl, and search whether there are other genes in the segment where the target gene is located on the chromosome according to this position; if there are other genes, continue to obtain these genes that overlap with the target gene Types of other genes, if the other genes are protein-coding genes, then the target gene is not suitable for designing a knockout scheme.

[0111] S122. Preprocessing the transcript of the target gene. The specific method is: obtain the transcript information of the target gene from Ensembl, and exclude non-coding protein transcripts and incomplete transcripts.

[0112] S123. Find out the protein coding region of each transcript, that is, CDS. The specific method...

Embodiment approach 3

[0129] Implementation Mode 3: Large Fragment Knockout Solution

[0130] (1) Determine the knockout region

[0131] S131. Determine whether the target gene is suitable for designing a knockout scheme. The specific method is as follows: obtain the position of the target gene on the chromosome from Ensembl, and search whether there are other genes in the segment where the target gene is located on the chromosome according to this position; if there are other genes, continue to obtain these genes that overlap with the target gene Types of other genes, if the other genes are protein-coding genes, then the target gene is not suitable for designing a knockout scheme.

[0132]S132. Preprocessing the transcript of the target gene. The specific method is: obtain the transcript information of the target gene from Ensembl, and exclude non-coding protein transcripts and incomplete transcripts.

[0133] S133. Find out the protein coding region of each transcript, that is, CDS. The speci...

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Abstract

The invention discloses an automatic screening method, system and device for gene editing sites and a storage medium. The automatic screening method comprises the steps: obtaining a gene name and a species name, and obtaining a gene sequence, transcript information and chromosome position information from a gene database; determining an alternative knocking area according to the position information and the transcript information; carrying out GC content and complexity analysis on the alternative knocking areas to determine knocking areas; sequencing the knock areas according to the quantity and the position information of the common transcripts; intercepting a knock region sequence from the gene sequence through the position information of the knock region according to the sequence; and obtaining all gRNAs of the knocking region sequence and corresponding specific scores and cutting efficiency scores from gRNA online design software, and determining and displaying editing sites of the gRNAs according to the specific scores and the cutting efficiency scores. According to the embodiment of the invention, the gene editing sites with good knockout effect, strong specificity and high cutting efficiency can be automatically and efficiently screened, and the method can be widely applied to the technical field of gene editing.

Description

technical field [0001] The present invention relates to the technical field of gene editing, in particular to an automatic screening method, system, device and storage medium for gene editing sites. Background technique [0002] CRISPR / Cas9 guides Cas9 endonuclease to cleave the PAM upstream of the target sequence by designing a specific guide RNA to recognize the target sequence, causing DNA double-strand breaks at the target site; after DNA double-strand breaks, the non-homologous ends of the cell are used to join (NHEJ) or homologous recombination (HDR) to repair the cleavage site to achieve gene knockout, knock-in or point mutation at the DNA level. CRISPR / Cas9 has become one of the hottest technologies in the field of life sciences due to its advantages of simple operation, low cost and editing efficiency. mice, pigs, rabbits, monkeys, etc.), zebrafish, stem cells, tumor cell lines, bacteria and fungi, etc. [0003] The design of the CRISPR / Cas9 knockout scheme seems ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/30G16B30/00
CPCG16B20/30G16B30/00
Inventor 许锦莹林剑锋刘晓凯黄秋凤
Owner 广州源井生物科技有限公司
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