ALIGNMENT NETWORKS AND ELECTRICAL NETWORKS

In the analysis of biological sequences there arises the question of a ttributing weights to each element of a set of objects in such a way t hat similar objects do not overly influence deductions based on the en tire set of objects. Since there is no known precise statement of this problem, we introduce two axioms that these weights should fulfill. I t is then easy to see that this formulation includes one commonly used method. Further we apply the axiomatic framework to the new problem o f attributing weights to alignments between two sequences. Viewing a s equence alignment as a directed network, an analogy to electrical netw orks is developed. This connection is used to prove the existence of t he weights and develop other characteristics of an alignment network.