#15 Probe design 2

Solved
closed
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3
2016-03-06
2006-12-05
Untergasser
No

It would be good if you could request that one of the primers goes over a certain nucleotide (great for RT-PCRs when you want to span a intron/exon boundary).

It would be great if there would be more flexibility in the primer included/target/excluded regions. It would be good if they could be selected independently in combination with the boundary tool.

Discussion

  • Steve Rozen

    Steve Rozen - 2006-12-06

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    I complete agree.

    I suggest we try to get some more molecular biologists and involved, and
    start a serious (and time-limited) requirements assessment / prioritiazation
    discussion.

     
  • Charles Plessy

    Charles Plessy - 2006-12-28

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    For designing primers over intron/exon junctions, I have cheated primer3 by indicating the splice junction (-10/+10) as a hybridisation oligo and relaxing the corresponding parameters (since the splice junction is not necessarly a good hybridisation oligo). The primers have not yet been tested in real life, but their design seems OK.

     
  • Untergasser

    Untergasser - 2016-02-23

    Included in latest version of primer3.

    I close this ticket.

     
  • Untergasser

    Untergasser - 2016-02-23
    • status: open --> closed
    • assigned_to: Untergasser
    • Group: --> Assess_priority
     
  • Untergasser

    Untergasser - 2016-02-23
    • Group: Assess_priority --> Solved
     
  • Untergasser

    Untergasser - 2016-03-06
    • discussion: enabled --> disabled