Multiple Sequence Alignment as a Facility Location Problem 1

Abstract. A connection is made between certain multiple sequence alignment problems and facility location problems, and the existence of a PTAS for these problems is shown. Moreover, it is shown that multiple sequence alignment with SP-score and fixed gap penalties is MAX SNP-hard. Key words: multiple sequence alignment, SP-score, Space-L Alignment problem, Switchboard Location problem, PTAS, smooth polynomial programmin