Finding Approximate Palindromes in Strings Quickly and Simply

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.)

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   TR 2004/162

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Bioinformatics
Abstract:
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] & [java code] of the 1st algorithm.
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© L. Allison   http://www.allisons.org/ll/   (or as otherwise indicated),
Faculty of Information Technology (Clayton), Monash University, Australia 3800 (6/'05 was School of Computer Science and Software Engineering, Fac. Info. Tech., Monash University, was Department of Computer Science, Fac. Comp. & Info. Tech., '89 was Department of Computer Science, Fac. Sci., '68-'71 was Department of Information Science, Fac. Sci.)
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