Finding Approximate Palindromes in Strings Quickly and Simply

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 TR 2004/162

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Lloyd Allison,
School of Computer Science and Software Engineering, Monash University, Clayton, Victoria, Australia 3800.
Technical Report 2004/162,
23 Nov. 2004 (draft 19 Sept.)

Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in O(k.n)-time where n is the length of the string and k is the number of ``errors'' allowed in the palindrome. Its worst-case time-complexity is O(n2) but this does not occur with real biological sequences. A more complex algorithm guarantees O(k.n) worst-case time complexity.
See [arxiv...pdf][12/'04] & [] of the 1st algorithm.

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