BioJava is a suite of libraries which is specifically designed for bioinformatics, described here:
BioJava: an Open-Source Framework for Bioinformatics
R.C.G. Holland; T. Down; M. Pocock; A. Prlić; D. Huen; K. James; S. Foisy; A. Dräger; A. Yates; M. Heuer; M.J. Schreiber Bioinformatics 2008; doi://10.1093/bioinformatics/btn397
Please read this paper.
For this practical, I have decided to use Biojava 3, which is a more recent version of this library. We will be working through parts of the Biojava 3 cookbook to achieve some biological tasks. The advantage of using a library such as BioJava, is that it is possible to achieve very complex tasks with very few method calls. The disadvantage is that you often have to read a lot of documentation to work out which method calls to use.
The assessment for this part of the module consists of code fulfilling the different tasks.