Space-Saving Strategies for Analyzing Biomolecular Sequences

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Space-Saving Strategies for Analyzing
Biomolecular Sequences

• Kun-Mao Chao (???)
• Department of Computer Science and Information
  Engineering
• National Taiwan University, Taiwan
• URL http//www.csie.ntu.edu.tw/kmchao

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Linear-space ideasHirschberg, 1975 Myers and
Miller, 1988
Partition line
m/2
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Two subproblems½ original problem size
m/4
m/2
3m/4
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Four subproblems¼ original problem size
m/4
m/2
3m/4
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Time and Space Complexity

• Space O(MN)
• TimeO(MN)(1 ½ ¼ ) O(MN)

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Band Alignment(Joint work with W. Pearson and W.
Miller)
Sequence A

Sequence B
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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)(111) O(NW log N)
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Band Alignment in Linear Space
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Parallelogram
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Parallelogram
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Yet another partition line
Band width W
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Yet another partition line
O(N)
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Arbitrary region
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Arbitrary region