I am currently doing some cloning into a vector. For variouse reasons I need to order not simply sense and antisense oligos with 5′ overhangs, but sense and antisense strands that overlap over a small nucleotide sequense. After I anneal them, I polymerase them using Klenow, cut them with restriction enzymes and then clone the cut insert into the vector.
To plan all this we use the GeneRunner software from 1994 which is quite insufficient to be honest and causes a lot of headaches and mistakes during planning.
I wonder what is the leading software in the market for doing this type of calculations? I heared something about Oligo 7 and Vector NTI, but I am not really sure…..