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Automatic parallelization knockout strategy sequence repeatability analysis method and system.

An analysis method and sequence repetition technology, applied in the field of gene knockout, can solve the problems of low accuracy, large amount of data, confusion and errors, etc., and achieve the effect of improving analysis and evaluation efficiency and reducing analysis time

Active Publication Date: 2020-01-14
广州赛业百沐生物科技有限公司
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0004] In view of this, the object of the present invention is to provide an automatic parallelized knockout strategy sequence repeatability analysis method and its system, to solve the problem of manual calculation in the prior art for repetitive analysis of knockout strategies, which not only wastes a lot of manpower and material resources, And when there is a lot of data, it is easy to cause confusion, mistakes, and technical problems of low accuracy

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  • Automatic parallelization knockout strategy sequence repeatability analysis method and system.
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  • Automatic parallelization knockout strategy sequence repeatability analysis method and system.

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Embodiment 1

[0034] Embodiment 1: refer to figure 2 , the first embodiment of the present invention provides an automatic parallelized knockout strategy sequence repeatability analysis method, including: step S1, according to the preset fragment length, divide the knockout strategy data information corresponding to each knockout strategy, and obtain The continuous sub-fragments in the knockout strategy data information; and, using the continuous sub-fragments containing repeating units as repeating sequences;

[0035] It should be noted that in a mouse gene sequence, there may be multiple different knockout strategies, so an in-depth analysis of all possible knockout strategies is required to obtain the optimal knockout strategy. Sequence repeatability analysis for the region corresponding to the knockout strategy of the gene sequence is an essential link to determine whether each knockout strategy is applicable. After the gene is knocked out according to the selected knockout strategy, ...

Embodiment 2

[0045] Embodiment 2: refer to Figure 3-5 , the second embodiment of the present invention provides an automatic parallelized knockout strategy sequence repeatability analysis method, based on the above-mentioned embodiment 1, the step S2, "according to the repeat sequence, determine the sequence repetition corresponding to the knockout strategy degrees" include:

[0046] Step S21, determining the base composition of the repeating unit, the interval type corresponding to the repeating unit, and the number of occurrences of the repeating unit in the knockout strategy data information;

[0047] Among them, the base refers to derivatives of purine and pyrimidine, which are components of nucleic acid, nucleoside, and nucleotide. The major bases of DNA and RNA are slightly different, with an important difference: Thymine is the major pyrimidine base of DNA and is extremely rare in RNA; conversely, uracil is the major pyrimidine base of RNA and is rare in DNA . The base includes ...

Embodiment 3

[0092] Embodiment 3: refer to Figure 6 , the third embodiment of the present invention provides an automatic parallelized knockout strategy sequence repeatability analysis method, based on the above-mentioned embodiment 2, the step S2, "according to the repeat sequence, determine the sequence repetition corresponding to the knockout strategy degree, so as to use the sequence repeatability to carry out sequence repeatability analysis", also include:

[0093] Step S3, using the sequence repetition degree as the score assignment result of the knockout strategy, and obtaining the knockout strategy data information with the assigned score according to the score assignment result, and extracting all the knockout strategy data information less than the preset preferred threshold. The knockout strategy corresponding to the sequence repetition degree is used as a screening set;

[0094] Step S4, taking the knockout strategy with the lowest sequence repeatability in the screening set ...

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Abstract

The invention provides an automatic parallelization knockout strategy sequence repeatability analysis method and system. The method comprises the following steps of: according to a preset fragment length, dividing knockout strategy data information corresponding to each knockout strategy to obtain continuous sub-fragments in the knockout strategy data information; taking the continuous sub-fragments containing the repetitive units as a repetitive sequence; and according to the repetitive sequence, determining a sequence repetition degree corresponding to the knockout strategy so as to carry out sequence repeatability analysis by utilizing the sequence repetition degree. According to the automatic parallelization knockout strategy sequence repeatability analysis method and system, the determination of the repetitive sequence in the target sequence region corresponding to different knockout strategies of the gene sequence is achieved, so that an evaluation way for scoring optimization ofdifferent knockout strategies based on the repetitive sequence is provided; and moreover, the analysis and evaluation efficiency of the knockout strategy of the gene base sequence is improved, and the analysis time is shortened.

Description

technical field [0001] The invention relates to the technical field of gene knockout, in particular to an automatic parallelized knockout strategy sequence repeatability analysis method and a system thereof. Background technique [0002] Repetitive sequence, that is, multiple copies of a gene sequence fragment, is also a fragment composed of a specific base sequence that exists repeatedly. In the natural state, the inactivation phenomenon does not occur in the repeated sequence, and the inactivation of the transgene in genetic engineering is related to multiple copies. It may be that the repeat sequences form different chromosomal position changes through ectopic pairing, which shrinks the chromosomes at the repeat sequence sites (chromatinization), hinders the contact between transcription factors and transgenes spatially, and makes genes in the Disabled. [0003] The formulation of traditional knockout strategies requires repeated analysis of the base sequence first, and...

Claims

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Application Information

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IPC IPC(8): G16B20/00
CPCG16B20/00G16B40/00G16B50/00H04L9/40Y02A90/10
Inventor 刘嘉惠黎妃凤
Owner 广州赛业百沐生物科技有限公司