Unlock instant, AI-driven research and patent intelligence for your innovation.

Method for predicting microsatellite PCR product specificity based on genome information

A genome and microsatellite technology, applied in the field of bioinformatics, can solve the problem of the number of unique PCR amplification products of the 3' terminal base of microsatellite primers, etc.

Active Publication Date: 2021-08-06
CHENGDU RES BASE OF GIANT PANDA BREEDING
View PDF7 Cites 0 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The current analysis methods based on the comparison of biological information databases cannot solve the problems of the uniqueness of the 3' end bases of microsatellite primers and the prediction of the number of PCR amplification products.

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Method for predicting microsatellite PCR product specificity based on genome information
  • Method for predicting microsatellite PCR product specificity based on genome information

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0024] according to figure 1 , 2 As shown, the present embodiment provides a method for predicting the specificity of microsatellite PCR products based on genomic information, comprising the following steps:

[0025] Step 1: Store the sequence of the genome in a separate dictionary, where the key of the dictionary is the number of the chromosome, and the value of the dictionary is the sequence of the chromosome;

[0026] Step 2: Define the function method of the reverse complementary sequence, first reverse the sequence, then convert all the sequences to uppercase, and then convert the base "A" to lowercase "t", base " T" is converted to lowercase "a", base "G" is converted to lowercase "c", base "C" is converted to lowercase "g", and finally all lowercase sequences are capitalized;

[0027] Step 3: Define the matching mode of the upstream and downstream primers. There are 4 forms in total when the primers match the genome;

[0028] Step 4: According to the set parameters a...

Embodiment 2

[0034] The present embodiment provides a program for predicting the specificity of microsatellite PCR products based on genome information, and the operation method of the program is as follows:

[0035] Step 1: Prepare the corresponding reference genome sequence and primer sequence;

[0036] Step 2: Set parameter 1: the ID of the primer (can be defined manually, the default is Primer);

[0037] Step 3: Set parameter 2: the number of matching bases at the 3' end of the primer (generally set to 7-15, the default is 10);

[0038] Step 4: Setting parameter 3: the maximum length of the simulated PCR product (set according to the target band of amplification, the default is 3000);

[0039] Step 5: Set the output file name 4: Set it according to user needs;

[0040] Step 6: The running command is: python SPE.V1.py-f[the path where the reference genome sequence is located]-F[upstream primer sequence]-R[downstream primer sequence]-P[parameter 1]-c[parameter 2]-l [Parameter 3] -o[the ...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

Abstract

The invention discloses a method for predicting microsatellite PCR product specificity based on genome information. The method comprises the following steps: firstly, storing a genome sequence in an independent dictionary; defining a function method of a reverse complementary sequence; according to set parameters, extracting primer 3'-terminal base sequences in four forms, and according to the sequence in the step 4, respectively matching all the sites of the four forms of the primer on the genome; listing all combinations of the first form and the second form, and meanwhile listing a third form and a fourth form; finally, according to set parameters, screening out all genome areas meeting the conditions, wherein the areas are actual sequences of amplified PCR products, and then performing subsequent specificity evaluation. According to the method, automatic conditional matching of upstream and downstream primers in a genome is realized, specific evaluation is carried out; the method has guiding significance on screening of microsatellite primers and paternity test evaluation of species.

Description

technical field [0001] The invention relates to the technical field of biological information, in particular to a method for predicting the specificity of microsatellite PCR products based on genome information. Background technique [0002] The traditional microsatellite primer design is divided into the following three steps: first obtain the DNA sequence of the target microsatellite; secondly obtain the optimal primer by primer design software; finally compare the upstream primer and the downstream primer to the reference genome respectively (mismatch base The number of bases is generally set to 1-2), and it is determined whether the primers have high specificity by checking the positions of the upstream and downstream primers on the genome. In addition, after the primers were synthesized, they were amplified by PCR and checked for the length of the amplified products by agarose gel electrophoresis. [0003] At present, the large-scale bioinformatics databases (NCBI, UCS...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
Patent Type & Authority Applications(China)
IPC IPC(8): G16B50/30G16B30/10
CPCG16B50/30G16B30/10
Inventor 李严沈富军张亮张紫阳王也寇洁刘红刘佳文王涓
Owner CHENGDU RES BASE OF GIANT PANDA BREEDING