Algorithms for sequence analysis via mutagenesis

Despite many successes of conventional DNA sequencing methods, some DNAs remain difficult or impossible to sequence. Unsequenceable regions occur in the genomes of many biologically important organisms, including the human genome. Such regions range in length from tens to millions of bases, and may contain valuable information such as the sequences of important genes. The authors have recently developed a technique that renders a wide range of problematic DNAs amenable to sequencing. The technique is known as sequence analysis via mutagenesis (SAM). This paper presents a number of algorithms for analysing and interpreting data generated by this technique.

Equational Reasoning as a Tool for Data Analysis

A combination of deductive reasoning, clustering, and inductive learning is given as an example of a hybrid system for exploratory data analysis. Visualization is replaced by a dialogue with the data.

Unlocking hidden genomic sequence

Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs.

Common multiples of complete graphs

A graph H is said to divide a graph G if there exists a set S of subgraphs of G, all isomorphic to H, such that the edge set of G is partitioned by the edge sets of the subgraphs in S. Thus, a graph G is a common multiple of two graphs if each of the two graphs divides G.

Superconducting Correlations in Metallic Nanoparticles: Exact Solution of the BCS Model by the Algebraic Bethe Ansatz

Superconducting pairing of electrons in nanoscale metallic particles with discrete energy levels and a fixed number of electrons is described by the reduced Bardeen, Cooper, and Schrieffer model Hamiltonian. We show that this model is integrable by the algebraic Bethe ansatz. The eigenstates, spectrum, conserved operators, integrals of motion, and norms of wave functions are obtained. Furthermore, the quantum inverse problem is solved, meaning that form factors and correlation functions can be explicitly evaluated. Closed form expressions are given for the form factors and correlation functions that describe superconducting pairing.

Maximum packings of K-v-K-u with triples

We construct, for all positive integers u, and v with u less than or equal to v, a decomposition of K-v - K-u (the complete graph on v vertices with a. hole of size u) into the maximum possible number of edge disjoint triangles.

The number of 4-cycles in 2-factorizations of K2n minus a 1-factor

In this paper we give a complete solution to problem of determining the number of 4-cycles in a 2-factorization of K-2n\ 1-factor. (C) 2000 Elsevier Science B.V. All rights reserved.

Decompositions of complete multipartite graphs into cycles of even length

Necessary and sufficient conditions for the existence of an edge-disjoint decomposition of any complete multipartite graph into even length cycles are investigated. Necessary conditions are listed and sufficiency is shown for the cases when the cycle length is 4, 6 or 8. Further results concerning sufficiency, provided certain small decompositions exist, are also given for arbitrary even cycle lengths.

Constructing a class of designs with proportional balance

Text serves as a sequel to 'Computational and Constructive Design Theory,' c1996; containing research papers and surveys of recent research work on design construction and computer-aided study of designs. For researchers in theory of computational designs.

The mu-way intersection problem for m-cycle systems

An m-cycle system of order upsilon is a partition of the edge-set of a complete graph of order upsilon into m-cycles. The mu -way intersection problem for m-cycle systems involves taking mu systems, based on the same vertex set, and determining the possible number of cycles which can be common to all mu systems. General results for arbitrary m are obtained, and detailed intersection values for (mu, m) = (3, 4), (4, 5),(4, 6), (4, 7), (8, 8), (8, 9). (For the case (mu, m)= (2, m), see Billington (J. Combin. Des. 1 (1993) 435); for the case (Cc,m)=(3,3), see Milici and Quattrochi (Ars Combin. A 24 (1987) 175. (C) 2001 Elsevier Science B.V. All rights reserved.

The metamorphosis of lambda-fold 4-wheel systems into lambda-fold 4-cycle systems

A 4-wheel is a simple graph on 5 vertices with 8 edges, formed by taking a 4-cycle and joining a fifth vertex (the centre of the 4-wheel) to each of the other four vertices. A lambda -fold 4-wheel system of order n is an edge-disjoint decomposition of the complete multigraph lambdaK(n) into 4-wheels. Here, with five isolated possible exceptions when lambda = 2, we give necessary and sufficient conditions for a lambda -fold 4-wheel system of order n to be transformed into a lambda -fold Ccyde system of order n by removing the centre vertex from each 4-wheel, and its four adjacent edges (retaining the 4-cycle wheel rim), and reassembling these edges adjacent to wheel centres into 4-cycles.

Star decompositions of cubes

Let Sk denote the complete bipartite graph K-1k and let e,, denote the ii-cube. We prove that the obvious necessary conditions for the existence of an S-k-decomposition of Q(n) are sufficient.