Study bioinformatics is like being jack of all trade so it is important you choose where it will be good backup of computer science, and natural science infrastructure and faculty. Especially having a good teachers in computer science is indispensible.
Few places in Europe where good (and @some places no tution fees) master bioinformatics courses and recommended are:
KU Leuven, Belgium
http://onderwijsaanbod.kuleuven.be/opleidingen/e/CQ_50269018.htm
ETH, Zurich
University of Copenhagen, Denmark
http://www.binf.ku.dk/programmes/Master
University of Helsinki, Finland
http://www.cs.helsinki.fi/en/mbi/
Stockholm University, Sweden
Universities in Netherlands
http://www.nbic.nl/education/msc-programmes/
TUM , Munich Germany
http://www.mastersportal.eu/studies/865/bioinformatics.html
University of Bergen, Norway
