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primer3-org / primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
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Getting different output from primer3plus and primer3 when using default setting #5

Closed pdpdpd closed 6 years ago

pdpdpd commented 6 years ago

Hi, We are trying to get the same primer output from primer3_core using as what we got on primer3plus. However, I tried to apply the same setting as we used on primer3plus and got different results. I tried default setting on both as well but still got different output. Since the newest version of primer3 manual is 2.4.0, is there any difference between default parameter settings in the current version of primer3plus and primer3? [I found that the primer3_core output is more restrict on optimal primer size btw] Thanks a lot!

untergasser commented 6 years ago

Hi, this is intended. The command line version parameters are set to have maximal backward compartibility, while primer3plus parameters are set to be optimal for primer selection by current knowledge. Best, Andreas

pdpdpd commented 6 years ago

Hi Andreas,

Thank you very much! I’m just wondering if and how we can change the parameters in command line version so that it can show the same output as the online version (the default output, to begin with). My labmates tested dozens of primers provided from the online version but not the command line one, so they really trust the online output more.. It will be great if we can do that! Really appreciated!

Best, Yidan

On May 15, 2018, at 12:23 PM, Andreas Untergasser notifications@github.com wrote:

Hi, this is intended. The command line version parameters are set to have maximal backward compartibility, while primer3plus parameters are set to be optimal for primer selection by current knowledge. Best, Andreas

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

ptranvan commented 5 years ago

Did you find the primer3plus settings ?

djhshih commented 4 years ago

See http://primer3.org/manual.html#differencePrimer3vsPrimer3Plus