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13.0 years ago
User 5037
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290
hi could someone please tell me what is the computational complexity of creating a dotplot ?
3
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13.0 years ago
Farhat
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2.9k
It will be quadratic in the length of the sequence. You are comparing every base to every other base. There are n(n-1)/2 comparisons to be made.
2
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13.0 years ago
Fabian Bull
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1.3k
The naive way is quadratic in the length of both length:
O(m * n)
where m is the length of sequence 1 and n is the length of sequence 2.
I would not be suprised if there is a fancy datastructure which could do the job in linear time.
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You can't escape comparing nucleotide of one sequence against all of the other in order to find interesting changes occurring between the two genomes/chromosomes .
Long time ago: A very wise man stated that a linear algorithm for LCS would be impossible yet it exists.