An efficient rank based approach for closest string and closest substring.
This paper aims to present a new genetic approach that uses rank distance for solving two known NP-hard problems, and to compare rank distance with other distance measures for strings. The two NP-hard problems we are trying to solve are closest string and closest substring. For each problem we build a genetic algorithm and we describe the genetic operations involved. Both genetic algorithms use a fitness function based on rank distance. We compare our algorithms with other genetic algorithms that use different distance measures, such as Hamming distance or Levenshtein distance, on real DNA sequences. Our experiments show that the genetic algorithms based on rank distance have the best results.
Faculty of Mathematics and Computer Science, University of Bucharest, Bucharest, Romania. ldinu@fmi.unibuc.ro
Liviu P
LP
Dinu
Radu
R
Ionescu
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D033481:Chromosomes, Mammalian / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D006801:Humans; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*