Standard protocols for gap repair cloning call for 30b upstream and downstream homology regions. We use 50b. We want to insert a library into a vector, but get very few transformants. (using pYES into BY4742 yeast on ura- minimal media)
BY cells can be difficult to work with. In many ways they don't behave as good yeast cells should. By the way, I found an article which gives some suggestions on how to improve gap repair in yeast. Maybe it is of use to you?
With best regards, Christian
Article Improved gap repair cloning in yeast: Treatment of the gappe...