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Primer design method and system

A design method and primer combination technology, applied in the field of gene technology, can solve the problems of logic confusion, operational redundancy, specific analysis redundancy, etc., and achieve the effects of increasing the evaluation of eigenvalues, improving the running speed, and comparing the results in detail.

Pending Publication Date: 2022-05-13
GENETALKS BIO TECH CHANGSHA CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] 1. Probes cannot be designed;
[0006] 2. It is impossible to evaluate whether the primers cover the polymorphic sites, let alone design primers covering the polymorphic sites;
[0007] 3. The specificity assessment is not accurate enough to predict the amplification efficiency, and the comparison results cannot be visualized
[0008] 4. Redundant specificity analysis: In order to perform specificity analysis, two comparisons were performed, redundant operations, confusing logic, difficult to understand, and a waste of time; although the number of primers is small, the second run time is very short, but The time to the second run increases exponentially as the number of primers increases

Method used

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  • Primer design method and system

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Experimental program
Comparison scheme
Effect test

Embodiment 1

[0059] A method for designing primers, the specific process can be found in figure 1 , including the following steps:

[0060] (1) The template sequence is automatically generated according to the input file, and the input file supports the following three types:

[0061] 1.1. Template sequence: No processing is required, and subsequent analysis is performed directly to generate candidate oligos.

[0062] 1.2. Target site and genome file: Extract a sequence of a certain length upstream and downstream of the target site according to the genome file, and use it as a template sequence for oligo design.

[0063] 1.3. Target region and genome file: Extract the sequence of the target region according to the genome file and use it as the template sequence for oligo design.

[0064] (2) Traverse all candidate primer sequences at different positions and with different lengths based on the template sequence.

[0065] (3) Evaluate the characteristics of each candidate primer, includin...

Embodiment 2

[0123] A method for designing primers and probes, the specific process can be found in figure 1 , including the following steps:

[0124] (1) The template sequence is automatically generated according to the input file, and the input file supports 3 types:

[0125] 1.1. Template sequence: No processing is required, and subsequent analysis is performed directly to generate candidate oligos.

[0126] 1.2. Target site and genome file: Extract a sequence of a certain length upstream and downstream of the target site according to the genome file, and use it as a template sequence for oligo design.

[0127] 1.3. Target region and genome file: Extract the sequence of the target region according to the genome file and use it as the template sequence for oligo design.

[0128] (2) Traverse all candidate oligos sequences according to different positions and different lengths based on the template sequence.

[0129] (3) Evaluate various characteristics of oligos, including: basic char...

Embodiment 3

[0209] A primer design system applied to embodiment 1 or 2: used to execute the steps of the primer design method of embodiment 1 or embodiment 2 through programming of computer equipment. Specifically, it includes the following program units:

[0210] (1) a candidate primer generating program unit, which is used for traversing the target template sequence according to different positions and different lengths to obtain the candidate primer sequence;

[0211] (2) a basic feature calculation program unit, used to calculate each basic feature value of each candidate primer, and score each basic feature value;

[0212](3) SNP eigenvalue calculation unit, used to calculate the eigenvalue of the SNP in the template sequence and the candidate oligos sequence, and score the SNP eigenvalue;

[0213] (4) A single oligo-specific eigenvalue calculation program unit, used to count the number of regions that each candidate oligo can bind to, and record the melting temperature Tm of each b...

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Abstract

The invention discloses a primer design method and system. The design method comprises the following steps: traversing to obtain candidate sequences; calculating a basic characteristic value, an SNP characteristic value and a single primer specificity characteristic value of each candidate primer; scoring is performed; selecting a candidate primer combination with a proper position; calculating each pair of candidate primer combinations, and calculating each characteristic value, a corresponding score and a comprehensive score between the combinations; and selecting the candidate primer combination with the highest comprehensive score in the region and outputting. According to the primer design method, the probe can be designed, whether the primer covers the polymorphic site or not can be evaluated, and the design of the primer with the polymorphic site located at the tail end 3 or the probe located at the two ends is avoided. The defects that in the patent application 201811591649. X, a probe cannot be designed, whether a primer covers a polymorphic site or not cannot be evaluated, the design of the primer covering the polymorphic site cannot be avoided, the specificity evaluation is not accurate enough, and the display is not visual enough are overcome.

Description

technical field [0001] The invention belongs to the field of gene technology, and relates to a primer design method and system. Background technique [0002] PCR is a method for enzymatically synthesizing specific DNA fragments in vitro. Due to the high temperature deformation, low temperature annealing and suitable temperature extension reactions, a cycle is formed, and the cycle is carried out, so that the target DNA can be rapidly amplified. It has strong specificity, high sensitivity and easy operation. Simple and other features. [0003] Before the PCR reaction, suitable primers must be designed. A primer is a short piece of single-stranded DNA or RNA, which serves as the origin of DNA replication and a polynucleotide chain that functions as a starting point for each polynucleotide chain to elongate during a nucleic acid synthesis reaction. The quality of the primer design directly affects the results of the entire experiment. The effect of primer design is affected ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16B40/00
CPCG16B20/20G16B40/00
Inventor 曾华萍王煜陈可欣朱碧银
Owner GENETALKS BIO TECH CHANGSHA CO LTD