Designing Primers: Finding Software to Test Primers

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SUMMARY

The discussion centers on finding software to test DNA primers, specifically highlighting the user's previous experience with the Mac program Amplify, which visualizes primer efficiency through virtual PCR products. The user expresses a need for alternatives after changing workplaces and not having access to Amplify. They mention Primer3 from MIT but express dissatisfaction with it, while also noting that DNA Stryder is an excellent tool for sequence manipulation, albeit only available for Mac users. The user ultimately finds Amplify again but is unable to use it due to platform limitations.

PREREQUISITES
  • Understanding of DNA primer design and testing
  • Familiarity with PCR (Polymerase Chain Reaction) concepts
  • Basic knowledge of software installation on PC and Mac
  • Experience with sequence manipulation tools
NEXT STEPS
  • Research alternatives to Amplify for PC users, such as SnapGene
  • Explore Primer3 documentation for advanced usage techniques
  • Investigate DNA Stryder features for Mac users
  • Learn about virtual PCR product visualization tools
USEFUL FOR

This discussion is beneficial for molecular biologists, bioinformaticians, and laboratory technicians involved in primer design and testing, particularly those seeking software solutions across different operating systems.

Monique
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Now I am looking for some software to test primers with. I always used to eye-ball a sequence, and based on that pick some good looking sequences, put it into the Mac program: Amplify.

This program then visualizes how specific and efficient the priming is on the target sequence by virtual pcr products.

BUT changed workplace, no Amplify.. I am trying to find it on the net though.

Does anyone now other programs which can handle the task? PC or Mac operatable?

I know of primer3 from MIT, but I don't like it..
 
Biology news on Phys.org
I have found the Amplify program!

http://www.cellbiol.com/soft.htm

too bad that I don't have a Mac :S

The DNA stryder is really good software too, for sequence manipulations, BUT only for Macs..
 
Tadaaaa!

Freeware for PCs
http://www.cellbiol.com/modules.php?op=modload&name=Downloads&file=index&req=viewsdownload&sid=5


Pretty cool site, cellbiol.com
 
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