Reports in Informatics Eecient Discovery of Conserved Patterns Using a Pattern Graph

EEcient discovery of conserved patterns using a pattern graph. Abstract We have earlier reported an algorithm JCH95] for discovering patterns conserved in sets of related protein sequences. The algorithm was implemented in a program called Pratt. It uses a depth rst search of the pattern space, together with a data structure making it possible to nd all segments matching a pattern very quickly (block data structure). Here we present a new search having two main advantages over the old strategy. Firstly it allows for easier integration with programs for multiple sequence alignment and data base search. Secondly, it makes it possible to use branch-and-bound search, and heuristics, to speed the search. The new search strategy has been implemented in a new version of the Pratt program.