Prof. Meirav Zehavi

We present a new pattern matching problem, the partial information query (PIQ) problem, which includes as special cases two problems that have important applications in bioinformatics: the alignment query (AQ) problem and the topology-free query (TFQ) problem. In both problems we have a pattern P and a graph H, and we seek a subgraph of H that resembles P. AQ requires knowing the topology of P, while TFQ ignores it. PIQ fits the scenario where partial information is available on the topology of P. Our main result is a parameterized algorithm for PIQ, which can handle inputs where P is a set of trees. It significantly improves the best known running time in solving TFQ. We also improve the best known running times in solving two special cases of AQ.