1) insert all intervals in an interval tree 2) construct a graph G with nodes for the intervals and edges between nodes if the intervals intersect (edge computation is done using the interval tree) 3) compute the connected components. 4) on each connected component construct the interval as the minimum and maximum coordinates of the corresponding intervals That can all be done in SeqAn.
That sounds neat. I'm going to look into it. Thanks a lot! Best, Fabian -- Fabian Buske Institute for Molecular Bioscience The University of Queensland Brisbane, Qld. 4072 Australia Phone: (61)-(7)-334-62608