A visualization tool to explore alphabet orderings for the Burrows-Wheeler Transform

The Burrows-Wheeler Transform (BWT) is an efficient invertible text transformation algorithm with the properties of tending to group identical characters together in a run, and enabling search of the text. This transformation has extensive uses particularly in lossless compression algorithms, indexing, and within bioinformatics for sequence alignment tasks. There has been recent interest in minimizing the number of identical character runs ($r$) for a transform and in finding useful alphabet orderings for the sorting step of the matrix associated with the BWT construction. This motivates the inspection of many transforms while developing algorithms. However, the full Burrows-Wheeler matrix is $O(n^2)$ space and therefore very difficult to display and inspect for large input sizes. In this paper we present a graphical user interface (GUI) for working with BWTs, which includes features for searching for matrix row prefixes, skipping over sections in the right-most column (the transform), and displaying BWTs while exploring alphabet orderings with the goal of minimizing the number of runs.Comment: 8 pages, 2 figure

Biomimetisch geprägte Hochleistungskeramiken für den Anlagenbau (BioCerAb): Abschlussbericht zum BMBF-Forschungsvorhaben

It was the overall aim of the compound project "Biomimetisch geprägte Hochleistungskeramiken für den An lagenbau" (BioCerAb), to prove, that biomimetically derived high efficiency ceramics for mechanical engineering and construction are feasible and also applicable. Within the course of the project it could be shown, that bionical pre-products for the manufacturing of ceramic components opennew perspectives in the field of ceramic technologies. As bionically derived pre-products, budget-friendly wood fibre boards could be used, which were converted into carbon through pyrofysis and consequently by reaction silicon treatment into ceramic SiSiC-components. One intrinsic aim of the entire project was, to display the entire production chain and to come to reach a cost efficient, lean production process, with which these newly developed ways of producing ceramic components was economically feasib le, ft was especially about producing big sized complex ceramic components for technical applications. The biogenic base material was planned to possibly convert the hierarchically organized biological structure through capillary silicon treatment into the desired clear cut microstructure of SiSiC-ceramics. In order to give proof of the feasibility of biomimetically derived high efficient ceramics for mechanical engineering and construction, two demonstration components were chosen: demonstrator component 1 was a complex, ceramic heat-exchanger, whereas demonstrator component 2 was a big-sized, ceramic wear protection from the field of pump construction. The two systems were chosen, because they form typical examples for the favourable use of ceramic materials in mechanical engineering and construction and which were as yet not disposable by means of conservative technology because of economic reasons and restricted possibilities of production. The two components in question were designed to show the broad variety of material and the technical applicability of biogenic ceramic material und the big-sized products manufactured from them, especially in the field of mechanical engineering and construction as well as plant engineering. It also gives a first insight into the new production technologies for these fields of application

Monomerizing alkali-metal 3,5-dimethylbenzyl salts with tris(N, N -dimethyl-2-aminoethyl)amine (MeTREN) : structural and bonding implications

The series of alkali-metal (Li, Na, K) complexes of the substituted benzyl anion 3,5-dimethylbenzyl (MeCHCH ) derived from 1,3,5-trimethylbenzene (mesitylene) have been coerced into monomeric forms by supporting them with the tripodal tetradentate Lewis donor tris(N,N-dimethyl-2-aminoethyl)amine, [N(CH CHNMe), MeTREN]. Molecular structure analysis by X-ray crystallography establishes that the cation-anion interaction varies as a function of the alkali-metal, with the carbanion binding to lithium mainly in a σ fashion, to potassium mainly in a π fashion, with the interaction toward sodium being intermediate between these two extremes. This distinction is due to the heavier alkali-metal forcing and using the delocalization of negative charge into the aromatic ring to gain a higher coordination number in accordance with its size. MeTREN binds the metal in a η mode at all times. This coordination isomerism is shown by multinuclear NMR spectroscopy to also extend to the structures in solution and is further supported by density functional theory (DFT) calculations on model systems. A MeTREN stabilized benzyl potassium complex has been used to prepare a mixed-metal ate complex by a cocomplexation reaction with tBuZn, with the benzyl ligand acting as an unusual ditopic σ/π bridging ligand between the two metals, and with the small zinc atom relocalizing the negative charge back on to the lateral CH arm to give a complex best described as a contacted ion pair potassium zincate

Synthesis of mono- and geminal dimetalated carbanions of bis(phenylsulfonyl) methane using alkali metal bases and structural comparisons with lithiated bis(phenylsulfonyl)imides

The alpha,alpha'-stabilized carbanion complexes [(PhSO2)(2)CHLi center dot THF] 1, [(PhSO2)(2)CHNa center dot THF] 2 and [(PhSO2)(2)CHK] 3 were prepared by the direct deprotonation of bis(phenylsulfonyl) methane I in THF with one molar equivalent of MeLi, BuNa and BnK respectively. The geminal dianionic complexes [(PhSO2)(2)CLi2 center dot THF] 4, [(PhSO2)(2)CNa2 center dot 0.55THF] 5 and [(PhSO2)(2)CK2] 6 were similarly prepared by the reaction of I with two molar equivalents of MeLi, BuNa and BnK respectively in THF. NMR and MS solution studies of 1 - 3 are consistent with the formation of charge-separated species in DMSO media. Solutions studies of 4 - 6, in conjunction with trapping experiments, indicate that the dianions deprotonate DMSO and regenerate the monoanions 1 - 3. Crystallographic analysis of 1 revealed a 1D chain polymer in which the metal centers are chelated by the bis( sulfonyl) ligands and connect to neighboring units through Li-O(S) interactions. An unexpected feature of 1 is that the polymeric chains are homochiral, since the chelating ligands of the backbone adopt the same relative configuration. Also, the phenyl substituents of each chelate in 1 are oriented in a cisoid manner. The sodium derivative 2 adopts a related solid-state structure, where enantiomeric pairs of chains combine to give a 1D ribbon motif. The lithium bis( phenylsulfonyl) imides [(PhSO2)(2)NLi center dot THF] 9 and [(PhSO2)(2)NLi center dot Pyr(2)] 10 were also prepared and structurally characterized. In the solid state 9 has a similar connectivity to that found for 1 but with heterochiral chains. In comparison, the more highly solvated complex 10 forms a 1D polymeric arrangement without chelation of the ligands and with the phenyl substituents oriented in a transoid fashion