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  • Degenerate primers desing software

    Hi all of you,

    I'm looking for a software to design degenerate primers to make a multiplex PCR to try to close a little genome who has 10 contigs. I tried to use some primers developers softwares but these couldn't give me what I want. Do somebody know a tool that could help me?

    thanks a lot

  • #3
    If you only have 10 gaps to close, and can guess the placement of some of them using a reference related species, then specific primers should be fine. I appreciate if you don't know which order the contigs run in, this could be harder.

    I would consider a mixed primer strategy - design up to 20 specific primers (both ends of each fragment) and do a mixed PCR (with multiple primers together) then size selection of any products. Talk to your lab colleagues about this.
    Last edited by maubp; 08-22-2012, 07:33 AM. Reason: typo

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    • #4
      Originally posted by rexxi View Post
      Hi all of you,

      I'm looking for a software to design degenerate primers to make a multiplex PCR to try to close a little genome who has 10 contigs. I tried to use some primers developers softwares but these couldn't give me what I want. Do somebody know a tool that could help me?

      thanks a lot
      Can you estimate the size of the gaps based on the genome size? In doing this type of work in the past, I found it really helps to know the expected gap size when optimizing PCR reactions. For example, if you expect a gap to be around 4kb, you would use a different set of conditions than if you expected a gap of 100 bp.

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