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  • Building a reference genome from scratch to use for primersearch !!!

    I have many primers that needs to be aligned to a reference genome in order to predicting it's PCR product by primersearch tool.

    the problem is I am working on olive tree which it's draft genome is not yet available .

    So I gathered all available sequences like EST (100 thousand ) and Genes (500)

    then I am trying now to align them to model genome like "Populus trichocarpa genome" in order to assemble them in a way I could build a reference genome.

    will this work and does it scientifically right or I could use the model genome it self as a reference rather than trying to create an olive genome reference ?!!!

  • #2
    Trying to align an olive tree to a poplar for assembly won't work. They need to be very close relatives, like, say, dog and wolf. You'd be better off with de-novo assembly from reads.

    P.S. Or more generally, perhaps the "can they interbreed" is a good criteria for reference-guided assemblies.
    Last edited by Brian Bushnell; 08-15-2014, 06:46 PM.

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