Determining DNA Sequence Similarity Using Maximum Independent Set Algorithms for Interval Graphs

Motivated by the problem of finding similarities in DNA and amino acid sequences, we study a particular class of two dimensional interval graphs and present an algorithm that finds a maximum weight “increasing” independent set for this class. Our class of interval graphs is a subclass of the graphs with interval number 2. The algorithm we present runs in O(n log n) time, where n is the number of nodes, and its implementation provides a practical solution to a common problem in genetic sequence comparison.

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