Primer design softwares and online websites you can't miss(with link)

PCR (Polymerase Chain Reaction) is a molecular biology technique used to amplify specific DNA fragments. Its biggest feature is that it can greatly increase a small amount of DNA. As the primary level for the upgrade of monsters on the scientific research road, PCR can be said to be the basic and the key of the basics. It is very mysterious for the newbie in the laboratory; for the veteran in the laboratory, it is very easy. So why is it not so laborious for the veterans, mainly they grasp the key to the PCR experiment-primer design.

The primer design largely determines the difficulty of the PCR experiment. There are also many primer design softwares that can quickly help you design primers. The editor has collected some primer design software and online websites here, and shared them with everyone in need.

Primer design softwares

1.Primer Premier

he main functions of Primer Premier software are divided into four types, namely GeneTank (sequence editing), Primer (primer design), Align (sequence comparison) and Enzyme (restriction analysis). Utilizing its advanced primer search, primer database, nested primer design, primer editing and analysis functions, you can design ideal primers with high-efficiency amplification capabilities, and you can also design primers for amplifying PCR products longer than 50kb.

The Chinese version of the manual link：

https://www.dxy.cn/bbs/newweb/pc/post/16260163

Primer Premier link：

https://www.dxy.cn/bbs/newweb/pc/post/33588285keywords=Primer+Premier%E8%BD%AF%E4%BB%B6%E4%B8%8B%E8%BD%BD。

2.Oligo7

The software is mainly used in the analysis and design of nucleic acid sequence primers, and calculates the hybridization temperature (Tm) of the nucleic acid sequence and theoretical prediction sequence at the same time. Its main functions include: searching for common primer pairs, designing sequencing primers, designing hybridization probes, and evaluating the quality of primer pairs, etc.

Oligo7 software link：

https://www.dxy.cn/bbs/newweb/pc/post/16260163

The Chinese version of the manual link：

https://wenku.baidu.com/view/202e54ea74a20029bd64783e0912a21614797fb6.html?fr=search-4-income1-psrec1&fixfr=L9XRL%2FuWrBjHS0IcsJ%2BCgQ%3D%3D

3.Beacon Designer

Beacon Designer is suitable for all qPCR analysis and can successfully design SYBR Green primers, TaqMan® probes, HRMA primers, MethyLight TaqMan®, LNA™ spiked TaqMan®, molecular beacons for standard and NASBA® detection, Scorpions® and FRET Probes, etc., are very powerful.

Beacon Designer software link：

https://www.dxy.cn/bbs/newweb/pc/post/40255439

Manual link：

https://www.dxy.cn/bbs/newweb/pc/post/22374814

4.circPrimer

CircPrimer is used to annotate circRNA and design software for detecting circRNA primers and specificity. CircPrimer software and user manual link：http://www.bioinf.com.cn/?p=1

Online websites

1.Gene-π

Gene-π, as a digital PCR learning exchange platform, was developed by the French company Stilla Technologies. Assist customers in interpreting digital PCR technology in an all-round way, realizing the advancement from novice to expert, suitable for all friends who are interested in digital PCR technology. At the same time provide primer probe design and basic knowledge guide of digital PCR technology.

link：https://www.gene-pi.com/

2.Primer3 Plus

Primer3 is a very simple but efficient online primer design website. Just paste the DNA sequence in the target sequence and click search. The primers can be screened by setting the product size, primer size, Tm range and other parameters.

link：http://www.primer3plus.com/

3.NCBI的Primer-Blast

NCBI's Primer-Blast

link：https://blast.ncbi.nlm.nih.gov/Blast.cgi

4.Primerbank

rimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). Contains more than 306,800 primers, covering the most famous human and mouse genes.

link：http://pga.mgh.harvard.edu/primerbank/

For the use of Primer3 Plus, Primer-Blast and Primerbank, please check this article link：

http://www.pinlue.com/article/2019/03/2916/078478362730.html

5.ICG（internal control genes）

ICG is a Wiki-based internal control gene (or reference gene) knowledge base, used for RT-qPCR standardization of multiple species. ICG conducts a comprehensive collection of internal control genes selected from a large amount of literature, and provides suitable internal control genes for model and non-model organisms.

link:http://icg.big.ac.cn/index.php/Main_Page

No matter which method is used to design primers and probes, it is only a parameter evaluation. The actual amplification efficiency and performance still need to be verified through experiments. The so-called "practice is the only criterion for testing truth." If you want to quickly obtain reliable primer probes, you can obtain resources from the hands of the seniors, or consult related literature. The primers in the literature have been verified by the author and verified by the journal review agency, which will most likely bring you an ideal result.

Finally, if you really can’t design it, you can still use the biological company to help. Cycloud Bio can provide you with comprehensive technical support and complete solutions. In addition, Cycloud Bio also provides you with a new type of Real-Time PCR system. The excellent product performance guarantees you to obtain true and reliable experimental data.