Lecture Notes in Computer Science, 2006, Volume 4288/2006, 100-110, DOI: 10.1007/11940128_12

A 6-Approximation Algorithm for Computing Smallest Common AoN-Supertree with Application to the Reconstruction of Glycan Trees

Kiyoko F. Aoki-Kinoshita, Minoru Kanehisa, Ming-Yang Kao, Xiang-Yang Li and Weizhao Wang

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Abstract

A node-labeled rooted tree T (with root r) is an all-or-nothing subtree (called AoN-subtree) of a node-labeled rooted tree T′ if (1) T is a subtree of the tree rooted at some node u (with the same label as r) of T′, (2) for each internal node v of T, all the neighbors of v in T′ are the neighbors of v in T. Tree T′ is then called an AoN-supertree of T. Given a set T={T1,T2,¼, Tn}{\mathcal {T}}=\{{T}_1,{T}_2,\cdots, {T}_n\} of nnode-labeled rooted trees, smallest common AoN-supertree problem seeks the smallest possible node-labeled rooted tree (denoted as LCST{\textbf{LCST}}) such that every tree T i in T{\mathcal {T}} is an AoN-subtree of LCST{\textbf{LCST}}. It generalizes the smallest superstring problem and it has applications in glycobiology. We present a polynomial-time greedy algorithm with approximation ratio 6.

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