The flybase dataset doesn't contain any of the sequence data, and we haven't tried querying residue sequences from within SPARQL yet. However, this is something we will need to do for a related project very shortly, so any experience or ideas you have would be very interesting to us. Querying residue sequences is not the most natural thing for SPARQL, so I anticipate some performance issues.
Sequence Ontology (http://genomebiology.com/2005/6/5/R44) might have a role to play here.
-Kei
