Abstract

Multiple alignment is an important problem in computational biology. It is well known that it can be solved exactly by a dynamic programming algorithm which in turn can be interpreted as a shortest path computation in a directed acyclic graph. The A algorithm (or goal directed unidirectional search) is a technique that speeds up the computation of a shortest path by transforming the edge lengths without losing the optimality of the shortest path. We implemented the A algorithm in a computer program similar to MSA [GKS95] and FMA [SI97b]. We incorporated in this program new bounding strategies for both, lower and upper bounds and show that the A algorithm, together with our improvements, can speed up computations considerably. Additionally we show that the A algorithm together with a standard bounding technique is superior to the well known Carillo-Lipman bounding since it excludes more nodes from consideration. 1 Introduction One of the most prominent problems in computational mo...

Citations