Method for positioning T-DNA insertion site by flag tag of sam file

A technology for inserting sites and tags, which is applied in the field of sam file flag tags to quickly locate T-DNA inserting sites, which can solve problems such as unsuitable for large-scale promotion, cumbersome steps, complex algorithms, etc., to eliminate false positive results and simple operation , low-cost effect

Active Publication Date: 2019-10-18
MAIZE RES INST SHANDONG ACAD OF AGRI SCI
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Problems solved by technology

[0006] The prior art algorithm is complex, time-consuming, cumbersome, and expensive, and is not suitable for large-scale promotion

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  • Method for positioning T-DNA insertion site by flag tag of sam file

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Embodiment Construction

[0031] In order to make the object, technical solution and advantages of the present invention more clear, the present invention will be further described in detail below in conjunction with the examples. It should be understood that the specific embodiments described here are only used to explain the present invention, not to limit the present invention.

[0032] In order to solve the problem of fast, free and efficient identification of T-DNA insertion sites, the present invention has developed a set of whole genome resequencing technology, using transgenic vectors for sequence comparison, screening according to the Flag tag of the comparison result file, and then A method for comparing the screened sequence with the Arabidopsis genome to finally obtain the T-DNA insertion site. The method has the characteristics of simple operation, time saving and high efficiency, low cost and accurate results.

[0033] The application principle of the present invention will be described ...

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Abstract

The invention belongs to the technical field of biology, and discloses a method for quickly positioning a T-DNA insertion site by a flag tag of a sam file. The method comprises the following steps: preparing a sample; carrying out whole genome re-sequencing; according to a sequencing result, obtaining a joint-removed clean_data; comparing a sequencing result with a transgenic vector sequence; according to the flag label of the comparison result file, removing sequences which are completely compared and cannot be compared to a carrier, and simultaneously removing labels which are compared for multiple times; extracting reads IDs and sequences of the screened flag tag values; and carrying out sequence alignment on the obtained sequence and an arabidopsis genome. According to a comparison result, a sequence which can be completely compared to an arabidopsis genome is removed; the remaining reads sequences are screened, and insertion sites are obtained; the false positive value in the insertion site is rejected and a final insertion site is obtained.

Description

technical field [0001] The invention belongs to the technical field of biological information processing, and in particular relates to a method for quickly locating a T-DNA insertion site with a flag tag of a sam file. Background technique [0002] Currently, the closest prior art: [0003] The use of T-DNA insertion to obtain transgenic plants is an important way to study the function of plant genes. But in most cases, the site of T-DNA insertion is unknown, it may be in the intergenic region, gene intron or exon, etc. At present, commonly used T-DNA insertion site identification methods include inverse PCR, semi-random primer PCR (such as Tail-PCR), etc. The above-mentioned traditional methods are relatively complicated to operate, take a long time, and have high technical requirements for experimenters. In addition, there is also the problem that the specificity is poor, and some T-DNA insertion mutations cannot obtain the insertion site. [0004] In recent years, with...

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Application Information

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IPC IPC(8): G16B20/30G16B30/10
CPCG16B20/30G16B30/10
Inventor 程文丁照华王志武赵素娴卢增斌尹昌果
Owner MAIZE RES INST SHANDONG ACAD OF AGRI SCI
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