P Systems with Minimal Left and Right Insertion and Deletion

In this article we investigate the operations of insertion and deletion performed at the ends of a string. We show that using these operations in a P systems framework (which corresponds to using specific variants of graph control), computational completeness can even be achieved with the operations of left and right insertion and deletion of only one symbol

P Systems with Minimal Left and Right Insertion and Deletion

Summary. In this article we investigate the operations of insertion and deletion performed at the ends of a string. We show that using these operations in a P systems framework (which corresponds to using specific variants of graph control), computational completeness can even be achieved with the operations of left and right insertion and deletion of only one symbol.

Fundamental Bounds and Approaches to Sequence Reconstruction from Nanopore Sequencers

Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic analysis of the impact of insertion-deletion (indel) errors in nanopore sequencers. In particular, we consider the following problems: (i) for given indel error characteristics and rate, what is the probability of accurate reconstruction as a function of sequence length; (ii) what is the number of `typical' sequences within the distortion bound induced by indel errors; (iii) using replicated extrusion (the process of passing a DNA strand through the nanopore), what is the number of replicas needed to reduce the distortion bound so that only one typical sequence exists within the distortion bound. Our results provide a number of important insights: (i) the maximum length of a sequence that can be accurately reconstructed in the presence of indel and substitution errors is relatively small; (ii) the number of typical sequences within the distortion bound is large; and (iii) replicated extrusion is an effective technique for unique reconstruction. In particular, we show that the number of replicas is a slow function (logarithmic) of sequence length -- implying that through replicated extrusion, we can sequence large reads using nanopore sequencers. Our model considers indel and substitution errors separately. In this sense, it can be viewed as providing (tight) bounds on reconstruction lengths and repetitions for accurate reconstruction when the two error modes are considered in a single model.Comment: 12 pages, 5 figure

Graph-Controlled Insertion-Deletion Systems

In this article, we consider the operations of insertion and deletion working in a graph-controlled manner. We show that like in the case of context-free productions, the computational power is strictly increased when using a control graph: computational completeness can be obtained by systems with insertion or deletion rules involving at most two symbols in a contextual or in a context-free manner and with the control graph having only four nodes.Comment: In Proceedings DCFS 2010, arXiv:1008.127

Fine-Structure Map of the Histidine Transport Genes in \u3cem\u3eSalmonella typhimurium\u3c/em\u3e

Afine-structure genetic map of the histidine transport region of the Salmonella typhimurium chromosome was constructed. Twenty-five deletion mutants were isolated and used for dividing the hisJ and hisP genes into 8 and 13 regions respectively. A total of 308 mutations, spontaneous and mutagen induced, have been placed in these regions by deletion mapping. The histidine transport operon is presumed to be constituted of genes dhuA, hisJ, and hisP, and the regulation of the hosP and hisJ genes by dhuA is discussed. The orientation of this operon relative to purF has been established by three-point crosses as being: purF duhA hisJ hisP

Brick polytopes, lattice quotients, and Hopf algebras

This paper is motivated by the interplay between the Tamari lattice, J.-L. Loday's realization of the associahedron, and J.-L. Loday and M. Ronco's Hopf algebra on binary trees. We show that these constructions extend in the world of acyclic $k$-triangulations, which were already considered as the vertices of V. Pilaud and F. Santos' brick polytopes. We describe combinatorially a natural surjection from the permutations to the acyclic $k$-triangulations. We show that the fibers of this surjection are the classes of the congruence $\equiv^k$ on $\mathfrak{S}_n$ defined as the transitive closure of the rewriting rule $U ac V_1 b_1 \cdots V_k b_k W \equiv^k U ca V_1 b_1 \cdots V_k b_k W$ for letters $a < b_1, \dots, b_k < c$ and words $U, V_1, \dots, V_k, W$ on $[n]$. We then show that the increasing flip order on $k$-triangulations is the lattice quotient of the weak order by this congruence. Moreover, we use this surjection to define a Hopf subalgebra of C. Malvenuto and C. Reutenauer's Hopf algebra on permutations, indexed by acyclic $k$-triangulations, and to describe the product and coproduct in this algebra and its dual in term of combinatorial operations on acyclic $k$-triangulations. Finally, we extend our results in three directions, describing a Cambrian, a tuple, and a Schr\"oder version of these constructions.Comment: 59 pages, 32 figure