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Issue No. 04 - October-December (2008 vol. 5)
ISSN: 1545-5963
pp: 503-513
Ron Y. Pinter , Technion - Israel Institute of Technology, Haifa
Antoni Lozano , Technical University of Catalonia, Barcelona
Gabriel Valiente , Technical University of Catalonia, Barcelona
Oleg Rokhlenko , Technion - Israel Institute of Technology, Haifa
Michal Ziv-Ukelson , Ben Gurion University of the Negev, Beer-Sheva
ABSTRACT
The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computational biology. Here we introduce a constrained form of this problem in which a partial mapping of a set of nodes (the "seeds") in one tree to a corresponding set of nodes in the other tree is given, and present efficient algorithms for both ordered and unordered trees. Whereas ordered tree matching based on seeded nodes has applications in pattern matching of RNA structures, unordered tree matching based on seeded nodes has applications in co-speciation and phylogeny reconciliation. The latter involves the solution of the planar tanglegram layout problem, for which a polynomial-time algorithm is given here.
INDEX TERMS
Graph algorithms, Graph Theory, Discrete Mathematics, Mathematics of Computing, Trees, Biology and genetics, Life and Medical Sciences, Computer Applications
CITATION
Ron Y. Pinter, Antoni Lozano, Gabriel Valiente, Oleg Rokhlenko, Michal Ziv-Ukelson, "Seeded Tree Alignment", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, no. , pp. 503-513, October-December 2008, doi:10.1109/TCBB.2008.59
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