title: An efficient method for multiple sequence alignment.
abstract: Multiple sequence alignment has been a useful method in the study of molecular evolution and sequence-structure relationships. This paper presents a new method for multiple sequence alignment based on simulated annealing technique. Dynamic programming has been widely used to find an optimal alignment. However, dynamic programming has several limitations to obtain optimal alignment. It requires long computation time and cannot apply certain types of cost functions. We describe detail mechanisms of simulated annealing for multiple sequence alignment problem. It is shown that simulated annealing can be an effective approach to overcome the limitations of dynamic programming in multiple sequence alignment problem.
authors.affiliation: Department of Computer Science, Michigan State University, East Lansing 48824-1027, USA.
authors.forename: J
authors.initials: J
authors.lastname: Kim
authors.forename: S
authors.initials: S
authors.lastname: Pramanik
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D003198:Computer Simulation; D006801:Humans; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software
chemical_list: D011506:Proteins