I have a problem with my proteomics homework. I was asked to design primers used to create a homologous recombination box to create PRP24-TAPtag yeast. I know that homologous regions should be 40-50nt and that my primer should include overhangs. I was told to base off of this publication: https://www.ncbi.nlm.nih.gov/pubmed/11403571
I have designed primers before, but this time I have encountered really big problems. I have found both my plasmid, pBS1479, TAPtag and PRP24 protein sequences, but I have no idea how should I join them to create primers and how to include the TAPtag. This is my first time using this method. Are there any tools I can use for this task? Should I add tag sequence to C end of my protein, then use plasmid seqence to create overhangs?