3,168 research outputs found

    On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

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    We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with pp processors. Given a static text of length nn, we first show how to compute the suffix array interval of a given pattern of length mm in O(mp+lgp+lglgplglgn)O(\frac{m}{p}+ \lg p + \lg\lg p\cdot\lg\lg n) time for pmp \le m. For approximate pattern matching with kk differences or mismatches, we show how to compute all occurrences of a given pattern in O(mkσkpmax(k,lglgn) ⁣+ ⁣(1+mp)lgplglgn+occ)O(\frac{m^k\sigma^k}{p}\max\left(k,\lg\lg n\right)\!+\!(1+\frac{m}{p}) \lg p\cdot \lg\lg n + \text{occ}) time, where σ\sigma is the size of the alphabet and pσkmkp \le \sigma^k m^k. The workhorse of our algorithms is a data structure for merging suffix array intervals quickly: Given the suffix array intervals for two patterns PP and PP', we present a data structure for computing the interval of PPPP' in O(lglgn)O(\lg\lg n) sequential time, or in O(1+lgplgn)O(1+\lg_p\lg n) parallel time. All our data structures are of size O(n)O(n) bits (in addition to the suffix array)

    Quark spectral properties above Tc from Dyson-Schwinger equations

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    We report on an analysis of the quark spectral representation at finite temperatures based on the quark propagator determined from its Dyson-Schwinger equation in Landau gauge. In Euclidean space we achieve nice agreement with recent results from quenched lattice QCD. We find different analytical properties of the quark propagator below and above the deconfinement transition. Using a variety of ansaetze for the spectral function we then analyze the possible quasiparticle spectrum, in particular its quark mass and momentum dependence in the high temperature phase. This analysis is completed by an application of the Maximum Entropy Method, in principle allowing for any positive semi-definite spectral function. Our results motivate a more direct determination of the spectral function in the framework of Dyson-Schwinger equations

    a simulation approach for a young german cohort

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    We quantify the private and fiscal lifetime returns to higher education in Germany accounting for the redistribution through the tax-and-transfer system, cohort effects, and the effect of income pooling within households. For this purpose we build a dynamic microsimulation model that simulates individual life cycles of a young German cohort in terms of several key variables, such as employment, earnings, and household formation. To estimate the returns to higher education, we link our dynamic microsimulation model to a tax-benefit simulator that allows converting gross wages into disposable incomes. On average, we find private and fiscal returns that are substantially higher than current market interest rates. However, analyzing the distribution of returns we also find that there is a considerable share of young adults for whom we forecast vocational training, the alternative to higher education, to be financially more rewarding. We demonstrate how the taxtransfer system and income pooling within couple households affect private returns and decompose the fiscal returns into its major components

    On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

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    We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with p processors. Given a static text of length n, we first show how to compute the suffix array interval of a given pattern of length m in O(m/p + lg p + lg lg p * lg lg n) time for p <= m. For approximate pattern matching with k differences or mismatches, we show how to compute all occurrences of a given pattern in O((m^k sigma^k)/p max (k, lg lg n) + (1+m/p) lg p * lg lg n + occ} time, where sigma is the size of the alphabet and p <= sigma^k m^k. The workhorse of our algorithms is a data structure for merging suffix array intervals quickly: Given the suffix array intervals for two patterns P and P\u27, we present a data structure for computing the interval of PP\u27 in O(lg lg n) sequential time, or in O(1 + lg_p lg n) parallel time. All our data structures are of size O(n) bits (in addition to the suffix array)

    MutationDistiller: user-driven identification of pathogenic DNA variants

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    MutationDistiller is a freely available online tool for user-driven analyses of Whole Exome Sequencing data. It offers a user-friendly interface aimed at clinicians and researchers, who are not necessarily bioinformaticians. MutationDistiller combines Mutation- Taster’s pathogenicity predictions with a phenotypebased approach. Phenotypic information is not limited to symptoms included in the Human Phenotype Ontology (HPO), but may also comprise clinical diagnoses and the suspected mode of inheritance. The search can be restricted to lists of candidate genes (e.g. virtual gene panels) and by tissue-specific gene expression. The inclusion of GeneOntology (GO) and metabolic pathways facilitates the discovery of hitherto unknown disease genes. In a novel approach, we trained MutationDistiller’s HPO-based prioritization on authentic genotype–phenotype sets obtained from ClinVar and found it to match or outcompete current prioritization tools in terms of accuracy. In the output, the program provides a list of potential disease mutations ordered by the likelihood of the affected genes to cause the phenotype. MutationDistiller provides links to gene-related information from various resources. It has been extensively tested by clinicians and their suggestions have been valued in many iterative cycles of revisions. The tool, a comprehensive documentation and examples are freely available at https://www.mutationdistiller.org
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