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We are pleased to present the proceedings of the Third Workshop on Algorithms in Bioinformatics (WABI 2003), which took place on September 15 20, 2003 in Budapest, Hungary. The WABI workshop was part of the four-conference meeting, ALGO 2003, which was locally organized by Dr. Jan os Csirik, Head of the Department of Computer Science, J ozsef Attila University, Budapest. See http: //www. conferences. hu/ALGO2003/algo_2003. htmfor more details. WABI focuses on discrete algorithms that address important problems in molecular biology, genomics, and genetics, that are founded on sound models,...