Technical Report CS-2013-01

Title: Partial Information Network Queries
Authors: Ron Y. Pinter and Meirav Zehavi
Abstract: We present a new pattern matching problem, the partial information query problem, which includes as special cases two problems that have important applications to bioinformatics: the alignment query problem and the weighted topology-free query problem. In both problems we have a pattern $P$ and a graph $H$, and we need to find a subgraph of $H$ that resembles $P$. An alignment query requires knowing the topology of $P$, while a weighted topology-free query ignores it. We provide a solution to users that have partial information regarding the topology of $P$. We present a fixed-parameter algorithm for this problem when $P$ is a set of trees, and improve the best known time complexities of the alignment query problem when $P$ is a path, of the alignment query problem when $P$ is a tree and of the weighted topology-free query problem.
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