First thing you have to look for might be if the Masters course is aimed at people that already have Bachelor in Bioinformatics or at peaople with a general Life Science degree. For example the course at the FU Berlin (were I did my Master) is aimed at students who already have a Bachelor in Bioinformatics so they will start with advanced computer science and statistics topics. The course at the University of Potsdam (probably also Hamburg) is aimed at people like you and starts with basic computer science and statistic course (they also give an intro to Perl and R).
Second there is a wide variety of different focused courses. For example the one at FU Berlin is (or was as they have changed the curriculum this year) focused on genomics and system biology and the computer science and mathematical side of things.
So I think the best way to choose a University will be to find out what the focus of the involved research groups is and see if that fits your own interests.
In some cases there is also a possibility to combine a Masters and PhD program like here .