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Space-Saving Strategies for Analyzing Biomolecular Sequences

Space-Saving Strategies for Analyzing Biomolecular Sequences. Kun-Mao Chao ( 趙坤茂 ) Department of Computer Science and Information Engineering National Taiwan University, Taiwan URL: http://www.csie.ntu.edu.tw/~kmchao. Linear-space ideas Hirschberg, 1975; Myers and Miller, 1988.

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Space-Saving Strategies for Analyzing Biomolecular Sequences

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  1. Space-Saving Strategies for Analyzing Biomolecular Sequences Kun-Mao Chao (趙坤茂) Department of Computer Science and Information Engineering National Taiwan University, Taiwan URL: http://www.csie.ntu.edu.tw/~kmchao

  2. Linear-space ideasHirschberg, 1975; Myers and Miller, 1988 Partition line m/2

  3. Two subproblems½ original problem size m/4 m/2 3m/4

  4. Four subproblems¼ original problem size m/4 m/2 3m/4

  5. Time and Space Complexity • Space: O(M+N) • Time:O(MN)*(1+ ½ + ¼ + …) = O(MN) 2

  6. Band Alignment(Joint work with W. Pearson and W. Miller) SequenceA SequenceB

  7. Band Alignment in Linear Space The remaining subproblems are no longer only half of the original problem. In worst case, this could cause an additional log N factor in time. O(log N) O(NW)*(1+1+…+1) =O(NW log N)

  8. Band Alignment in Linear Space

  9. Parallelogram

  10. Parallelogram

  11. Yet another partition line Band width W

  12. Yet another partition line O(N)

  13. Arbitrary region

  14. Arbitrary region

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