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

[smahmoud]

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 ?!!!

[Brian Bushnell]

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.