In this article we address two pattern matching problems which have important applications to bioinformatics. First we address the topology-free query problem: Given a set of labels L, a multiset P of labels from L, a graph H = (VH , EH) and a function LabelH : VH → 2, we need to find a subtree S of H which is an occurrence of P . We provide a fixed-parameter algorithm with parameter k = |P | w...