PCR Primer Designing | NCBI Primer BLAST | In silico PCR primer designing and validation
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Published 2020-08-05
PCR is a commonly used method to amplify DNA of interest in many fields such as biomedical research, diagnostic testing and forensic testing. While the outcome of PCR can be influenced by many other conditions such as the template DNA preparation and reaction conditions, designing a good pair of primers is a critical factor, A general requirement is that primers should have similar melting temperatures (Tm) and a balanced G/C content, but should avoid self-complementarity and hair-pin structure.
A number of public software tools have been developed to aid the primer design process. Notably, the widely used Primer3 program designs primers based on a variety of parameters. Since it does not perform target analysis, users typically need to test the primer specificity using additional tools. However, this process is time-consuming and sometimes even impractical if the primers have too many database matches. NCBI Primer BLAST is vergood tool, it not only gives us a predicted primer list, but also provides a specific target analysis.
NCBI Primer BLAST: www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi
Primer Stat: sites.ualberta.ca/~stothard/javascript/pcr_primer_…
Reverse Complement: www.bioinformatics.org/sms/rev_comp.html
Literature": link.springer.com/chapter/10.1007/978-3-030-02634-…
Facebook: www.facebook.com/groups/261045198486665/
Instagram: www.instagram.com/bioinformatics.bb/
All Comments (21)
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Thanks, Prof. This is the most comprehensive video on primer design I have ever watched.
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Very well explained, covering both primer design and validation! Worth viewing for beginners!
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Thank you so much Prof BB, this was super helpful!
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Hello Sir, Your tutorial on PCR Primer designing is awesome and you cover all single details regarding it. I searched a lot and i found your tutorial on primer designing that is easy to understand. It is requested that kindly upload a tutorial on ARMS PCR primer designing as well. I am sure your tutorial on ARMS PCR will be very helpful and beneficial for me. Kindly do me a favour sir upload the video ASAP. Thankyou for your anticipation.
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This video was really very helpful for beginner's. Thanks a lot for sharing everything in detail and hoping to see more tutorials like this.
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You helped me complete my assignment, Thank you so much!
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my pleasure to call you real a prof. of Abstract solver in Primer design.
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Hi sir I'm biggest fan for your teaching. You are just outstanding teacher
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Thanks for the refresher. It was certainly worthwhile. Thanks so very much.
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Very well explained sir. Congratulations and expecting many more for genetics community.
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really great ,,it will be appreciating if you will describe vector designing also
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Thank you sir.
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What a useful video thank you !
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thanks for this video sir, it is helped me a lot. please make a video if possible on Primer designing for Expression vectors and identification of ER sites for cloning.
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Thank you so much for this information sir...it helped me alot
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Great explanation
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You literallyyyy saveeeeeed me ❣️
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Sir, what if we want to introduce a restriction site in the primer for cloning. What should we do then?
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Thank you, sir.
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Very informative
