Title :
Seeded Tree Alignment
Author :
Lozano, Antoni ; Pinter, Ron Y. ; Rokhlenko, Oleg ; Valiente, Gabriel ; Ziv-Ukelson, Michal
Author_Institution :
Dept. of Software, Tech. Univ. of Catalonia, Barcelona
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.
Keywords :
biology computing; macromolecules; molecular biophysics; molecular configurations; trees (mathematics); RNA structure alignment; comparative phylogenetics; computational biology; polynomial-time algorithm; seeded tree alignment; unordered tree matching; Biology and genetics; Computer Applications; Discrete Mathematics; Graph Theory; Graph algorithms; Life and Medical Sciences; Mathematics of Computing; Trees; Algorithms; Base Sequence; Evolution, Molecular; Molecular Sequence Data; Phylogeny; RNA; Ribonuclease P; Sequence Alignment; Sequence Analysis, RNA;
Journal_Title :
Computational Biology and Bioinformatics, IEEE/ACM Transactions on
DOI :
10.1109/TCBB.2008.59
