RNA tree comparisons via unrooted unordered alignments

Authors:
Nimrod Milo;Shay Zakov;Erez Katzenelson;Eitan Bachmat;Yefim Dinitz;Michal Ziv-Ukelson
Affiliations:
Dept. of Computer Science, Ben-Gurion University of the Negev, Israel;Dept. of Computer Science and Engineering, UC San Diego, La Jolla, CA;Dept. of Computer Science, Ben-Gurion University of the Negev, Israel;Dept. of Computer Science, Ben-Gurion University of the Negev, Israel;Dept. of Computer Science, Ben-Gurion University of the Negev, Israel;Dept. of Computer Science, Ben-Gurion University of the Negev, Israel
Venue:
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Year:
2012

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Abstract

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(nTnS min (dT, dS)) time complexity, where nT and nS are the number of nodes and dT and dS 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.