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#14 Primer Dimer Prediction

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nobody
2
2013-02-05
2006-12-05
Untergasser
No

Probably this goes hand in hand with secondary structure prediction:

Primers picked with primer3 have sometimes high primer dimer potential if they are checked with Beacon Designer.

Maybe we could put the self and crossannealing on a more thermodynamic basis? Or improve it?

Discussion

  • Steve Rozen
    Steve Rozen
    2006-12-06

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    I completely agree. I am not sure where to prioritize this.

    I do not know Beacon Designer.

    I would say this partly comes under requirements assessment / prioritization.

     
  • Onkel D.
    Onkel D.
    2007-01-05

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    Here a link to the program "AutoDimer" which is designed to predict primer dimers and other features:
    http://www.cstl.nist.gov/div831/strbase/AutoDimerHomepage/AutoDimerProgramHomepage.htm

    I don't know the author of that software, but maybe this could somehow be included / linked to Primer3?