An Evolutionary Algorithm for the Maximum Weight Trace Formulation of the Multiple Sequence Alignment Problem

Abstract. The multiple sequence alignment problem (MSA) can be reformulated as the problem of finding a maximum weight trace in an alignment graph, which is derived from all pairwise alignments. We improve the alignment graph by adding more global information. A new construction heuristic and an evolutionary algorithm with specialized operators are proposed and compared to three other algorithms for the MSA, indicating advantages of the new approaches.

• Type: Conference
• Year: 2004
• Where: PPSN
• Authors: Gabriele Koller, Günther R. Raidl
• Keywords: Alignment Graph, Distributed And Parallel Computing, Maximum Weight Trace, PPSN 2004, Sequence Alignment Problem