An Efficient Method for Multiple Sequence Alignment

Multiple sequence alignment has been a useful methodin the study of molecular evolution and sequence-structure relationships. This paper presents a newmethodfor multiple sequence alignment based on simulated annealing technique. Dynamicprogramming has been widely used to find an optimal alignment. However, dynamicprogramminghas several limitations to obtain optimalalignment. It. requires long computation time and cannot apply certain types of cost functions. Wedescribe detail mechanismsof simulated annealing for multiple sequencealignment. problem.It is shownthat simulatedannealing can be an effective approachto overcomethe limitations of dynamicprogrammingin multiple sequence alignment problem. Key words, computational complexity, dynamic programming, multiple sequence alignment, protein sequenceanalysis, sequencesimilarity.

• Type: Conference
• Year: 1994
• Where: ISMB
• Authors: Jin Kim, Sakti Pramanik
• Keywords: Computational Biology, ISMB 1994, Multiple Sequence Alignment, Sequence Alignment Problem, Simulated Annealing