APPROXIMATE MATCHING OF NETWORK EXPRESSIONS WITH SPACERS

We present two algorithmic results pertinent to the matching of patterns of interest in macromolecular sequences. The first result is an output sensitive algorithm for approximately matching network expressions, i.e., regular expressions without Kleene closure. This result generalizes the O (kn) expected-time algorithm of Ukkonen for approximately matching keywords [Ukk85]. The second result concerns the problem of matching a pattern that is a network expression whose elements are approximate matches to network expressions interspersed with specifiable distance ranges. For this class of patterns, it is shown how to determine a backtracking procedure whose order of evaluation is optimal in the sense that its expected time is minimal over all such procedures.