I would like to write the BLAST Search algorithm using BioJava for a school project.
I can not find any sources, tutorials, nothing in the BioJava Cookbook. I would like to specify the query and target sequences, and find the similar subsequences.
Can anybody give me some pointers?
Well, implementing a very basic BLAST is not that hard. Perhaps this is still challenging for a first-year PhD, but a sophisticated programmer may write a basic one in a week.
Do you really want to re-implement the BLAST algorithm, or rather call BLAST from within BioJava? The former is an extremely epic task, as BLAST has a >20 year history of development and refinement, which you'll not be able to mirror in any reasonable amount of time.