There are two examples that we will provide:


1.)    Custom Primer Design


In this case, a small genome is provided, and primers are designed across the whole genome.


2.)    Generic Primer Design


In this case, you are designing primers for an organism that is in Ensembl.You can then take advantage of using Ensembl, HUGO, or rsSNP IDís to specify your targets.In order to run the Generic Primer Design, you will need to download the entire reference.Since these Ensembl reference genomes may be quite large, they are not part of this distribution that you downloaded.


For more information on the difference between the two main setups please read the PCR_Primer_Design-README.doc in the primer_design directory.


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