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Numerous algorithmic problems arise in Bioinformatics over and above [alignment], [evolutionary] trees etc..
The longest biased interval (LBI) problem is to find long intervals in a sequence that are of biological interest because they have significantly biased base-composition.
Approximate palindromes in DNA may code for miRNAs or have other biological functions.
Some "classic" Computer Science algorithms and data structures are also useful in Bioinformatics, for example,
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