Abstract
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.
Supported by NSF Presidential Young Investigator Grant DCR-8451387.
Partially supported by FAPESP, Brazil, under grant 87/0197-2.
Supported by Wisconsin Alumini Research Foundation and by National Science Foundation under grant CCR-9024516
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© 1992 Springer-Verlag Berlin Heidelberg
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Joseph, D., Meidanis, J., Tiwari, P. (1992). Determining DNA sequence similarity using maximum independent set algorithms for interval graphs. In: Nurmi, O., Ukkonen, E. (eds) Algorithm Theory — SWAT '92. SWAT 1992. Lecture Notes in Computer Science, vol 621. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-55706-7_29
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DOI: https://doi.org/10.1007/3-540-55706-7_29
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