Multiple Genome Alignment: Chaining Algorithms Revisited

  • Mohamed Ibrahim Abouelhoda
  • Enno Ohlebusch
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2676)


Given n fragments from k > 2 genomes, we will show how to find an optimal chain of colinear non-overlapping fragments in time O(n logk−2 n log log n) and space O(n logk−2 n). Our result solves an open problem posed by Myers and Miller because it reduces the time complexity of their algorithm by a factor log2 n / log log n and the space complexity by a factor log n. For k = 2 genomes, our algorithm takes O(n log n) time and O(n) space.


Range Query Priority Queue Longe Common Subsequence Range Tree Longe Common Subsequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Mohamed Ibrahim Abouelhoda
    • 1
  • Enno Ohlebusch
    • 2
  1. 1.Faculty of TechnologyUniversity of BielefeldBielefeldGermany
  2. 2.Faculty of Computer ScienceUniversity of UlmUlmGermany

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