[Biojava-l] how do you run a similarity search through biojava classes?

[Alberto Ambesi]

I need to find the best similarity match of a query sequence against 
bigger sequence (say, a chromosome region of 100 kb). what I need as 
output is the identity % of the match and the position (start/end).
please any suggestions or sample code are apreciated.
Thank you,
Alberto Ambesi