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do not seem to be sucient. Thus, multiple protein structure alignment should be studied further. In this paper, each protein structure is treated as a rigid body. That is, alignments are computed considering global positions only. Although such a treatment is adequate for comparing structures with strong similarities, it seems to be inadequate for comparing(More)
In this paper, we consider an integer convex optimization problem where the objective function is the sum of separable convex functions (that is, of the form Σ (i,j)∈Q ij ij F (w) + Σ i∈P i i B () µ), the constraints are similar to those arising in the dual of a minimum cost flow problem (that is, of the form µ i-µ j ≤ w ij , (i, j) ∈ Q), with lower and(More)
A physical map has been constructed of the human genome containing 15,086 sequence-tagged sites (STSs), with an average spacing of 199 kilobases. The project involved assembly of a radiation hybrid map of the human genome containing 6193 loci and incorporated a genetic linkage map of the human genome containing 5264 loci. This information was combined with(More)
We present a simple sequential algorithm for the maximum flow problem on a network with n nodes, m arcs, and integer arc capacities bounded by U. Under the practical assumption that U is polynomially bounded in n, our algorithm runs in time O(nm + n 2 log n). This result improves the previous best bound of O(nm log(n 2 /m)), obtained by Goldberg and Taran,(More)
Efficient implementations of Dijkstra's shortest path algorithm are investigated. A new data structure, called the <italic>radix heap</italic>, is proposed for use in this algorithm. On a network with <italic>n</italic> vertices, <italic>m</italic> edges, and nonnegative integer arc costs bounded by <italic>C</italic>, a one-level form of radix heap gives a(More)
In this paper we suggest new scaling algorithms for the assignment and minimum mean cycle problems. Our assignment algorithm is based on applying scaling to a hybrid version of the recent auction algorithm of Bertsekas and the successive shortest path algorithm. The algorithm proceeds by relaxing the optimality conditions, and the amount of relaxation is(More)
In this paper, we study network ow algorithms for bipartite networks. A network G = (V;E) is called bipartite if its vertex set V can be partitioned into two subsets V 1 and V 2 such that all edges have one endpoint in V 1 and the other in V 2. Let n = jV j, n 1 = jV 1 j, n 2 = jV 2 j, m = jEj and assume without loss of generality that n 1 n 2. We call a(More)