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TreeRank: a similarity measure for nearest neighbor searching in phylogenetic databases

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4 Author(s)
Wang, J.T.L. ; Coll. of Comput. Sci., New Jersey Inst. of Technol., Newark, NJ, USA ; Huiyuan Shan ; Shasha, D. ; Piel, W.H.

Phylogenetic trees are unordered labeled trees in which each leaf node has a label and the order among siblings is unimportant. In this paper we propose a new similarity measure, called TreeRank, for phylogenetic trees and present an algorithm for computing TreeRank scores. Given a query or pattern tree P and a data tree D, the TreeRank score from P to D is a measure of the topological relationships in P that are found to be the same or similar in D. The proposed algorithm calculates the TreeRank score in O(M2 + N) time where M is the number of nodes appearing in both P and D, and N is the number of nodes in D. We then develop a search engine that, given a query or pattern tree P and a database of trees D, finds and ranks the nearest neighbors of P in D where the "nearness" is measured by the proposed similarity function. This structure-based search engine is fully operational and is available on the World Wide Web.

Published in:

Scientific and Statistical Database Management, 2003. 15th International Conference on

Date of Conference:

9-11 July 2003