RNA tree comparisons via unrooted unordered alignments

Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


We generalize some current approaches for RNA tree alignment, which are traditionally confined to ordered rooted mappings, to also consider unordered unrooted mappings. We define the Homeomorphic Subtree Alignment problem, and present a new algorithm which applies to several modes, including global or local, ordered or unordered, and rooted or unrooted tree alignments. Our algorithm generalizes previous algorithms that either solved the problem in an asymmetric manner, or were restricted to the rooted and/or ordered cases. Focusing here on the most general unrooted unordered case, we show that our algorithm has an O(n T n S min (d T, d S)) time complexity, where n T and n S are the number of nodes and d T and d S are the maximum node degrees in the input trees T and S, respectively. This maintains (and slightly improves) the time complexity of previous, less general algorithms for the problem. Supplemental materials, source code, and web-interface for our tool are found in http://www.cs.bgu.ac.il/~negevcb/FRUUT.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 12th International Workshop, WABI 2012, Proceedings
Number of pages14
StatePublished - 1 Oct 2012
Event12th International Workshop on Algorithms in Bioinformatics, WABI 2012 - Ljubljana, Slovenia
Duration: 10 Sep 201212 Sep 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7534 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference12th International Workshop on Algorithms in Bioinformatics, WABI 2012

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)


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