Combinatorial Pattern Matching

Volume 3537 of the series Lecture Notes in Computer Science pp 190-200

DNA Compression Challenge Revisited: A Dynamic Programming Approach

  • Behshad BehzadiAffiliated withLIX, Ecole Polytechnique
  • , Fabrice Le FessantAffiliated withLIX, Ecole Polytechnique

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Standard compression algorithms are not able to compress DNA sequences. Recently, new algorithms have been introduced specifically for this purpose, often using detection of long approximate repeats. In this paper, we present another algorithm, DNAPack, based on dynamic programming. In comparison with former existing programs, it compresses DNA slightly better, while the cost of dynamic programming is almost negligible.