Chaining algorithms for multiple genome comparison

@article{Abouelhoda2005ChainingAF,
  title={Chaining algorithms for multiple genome comparison},
  author={Mohamed Ibrahim Abouelhoda and Enno Ohlebusch},
  journal={J. Discrete Algorithms},
  year={2005},
  volume={3},
  pages={321-341}
}
Given n fragments from k > 2 genomes, Myers and Miller showed how to find an optimal global chain of colinear non-overlapping fragments in O(n log n) time and O(n log n) space. For gap costs in the L1-metric, we reduce the time complexity of their algorithm by a factor log 2 n log log n and the space complexity by a factor log n. For the sum-of-pairs gap cost, our algorithm improves the time complexity of their algorithm by a factor log n log log n . A variant of our algorithm finds all… CONTINUE READING

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