Seeded tree alignment

Antoni Lozano; Ron Y. Pinter; Oleg Rokhlenko; Gabriel Valiente; Michal Ziv-Ukelson

doi:10.1109/TCBB.2008.59

Seeded tree alignment

Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson

Department of Computer Science

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

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 cospeciation and phylogeny reconciliation. The latter involves the solution of the planar tanglegram layout problem, for which a polynomial-time algorithm is given here.

Original language	English
Article number	4540091
Pages (from-to)	503-513
Number of pages	11
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume	5
Issue number	4
DOIs	https://doi.org/10.1109/TCBB.2008.59
State	Published - 1 Oct 2008

Keywords

Comparative phylogenetics
RNA structure alignment
Tanglegram layout
Tree matching

ASJC Scopus subject areas

Biotechnology
Genetics
Applied Mathematics

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10.1109/TCBB.2008.59

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title = "Seeded tree alignment",

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 cospeciation and phylogeny reconciliation. The latter involves the solution of the planar tanglegram layout problem, for which a polynomial-time algorithm is given here.",

keywords = "Comparative phylogenetics, RNA structure alignment, Tanglegram layout, Tree matching",

author = "Antoni Lozano and Pinter, {Ron Y.} and Oleg Rokhlenko and Gabriel Valiente and Michal Ziv-Ukelson",

note = "Funding Information: The research described in this paper has been supported in part by the Spanish Ministry of Education and Science Projects TIN 2004-07925-C03-01 GRAMMARS, TIN2004-04343 iDEAS, TIN2005-08832-C03-03 MOISES-BAR, MTM2006-07773 COMGRIO, and PCI2006-A7-0614. The work of Michal Ziv-Ukelson was supported in part by the Israeli Ministry of Science and Technology under an Eshkol grant.",

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AU - Lozano, Antoni

AU - Pinter, Ron Y.

AU - Rokhlenko, Oleg

AU - Valiente, Gabriel

AU - Ziv-Ukelson, Michal

N1 - Funding Information: The research described in this paper has been supported in part by the Spanish Ministry of Education and Science Projects TIN 2004-07925-C03-01 GRAMMARS, TIN2004-04343 iDEAS, TIN2005-08832-C03-03 MOISES-BAR, MTM2006-07773 COMGRIO, and PCI2006-A7-0614. The work of Michal Ziv-Ukelson was supported in part by the Israeli Ministry of Science and Technology under an Eshkol grant.

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N2 - 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 cospeciation and phylogeny reconciliation. The latter involves the solution of the planar tanglegram layout problem, for which a polynomial-time algorithm is given here.

AB - 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 cospeciation and phylogeny reconciliation. The latter involves the solution of the planar tanglegram layout problem, for which a polynomial-time algorithm is given here.

KW - Comparative phylogenetics

KW - RNA structure alignment

KW - Tanglegram layout

KW - Tree matching

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Seeded tree alignment

Abstract

Keywords

ASJC Scopus subject areas

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