I want to transfer a whole mutant GFP library under arbinose inducible promoter on a pBAD backbone to pMAL p2x backbone under tac promoter? What is the best method for this? What is typical % of recovery for such process?
I presume you have plenty of DNA from the library or can amplify and get it. So you should have ample source of insert to reclone your library. At the end it will very much depend upon how well you carry out the cloning and transformation and the final number of colonies you recover. So you can't really predict what is the % recovery because it all depends on how many you end up with. But if you have 5-10 fold more than the original complexity then you probably have preserved most of the library.