Bidirectional best hit r-window gene clusters

<p>Abstract</p> <p>Background</p> <p><it>Conserved gene clusters </it>are groups of genes that are located close to one another in the genomes of several species. They tend to code for proteins that have a functional interaction. The identification of conserved gene clusters is an important step towards understanding genome evolution and predicting gene function.</p> <p>Results</p> <p>In this paper, we propose a novel pairwise gene cluster model that combines the notion of bidirectional best hits with the <it>r</it>-window model introduced in 2003 by Durand and Sankoff. The bidirectional best hit (BBH) constraint removes the need to specify the minimum number of shared genes in the <it>r</it>-window model and improves the relevance of the results. We design a subquadratic time algorithm to compute the set of BBH <it>r</it>-window gene clusters efficiently.</p> <p>Conclusion</p> <p>We apply our cluster model to the comparative analysis of <it>E. coli </it>K-12 and <it>B. subtilis </it>and perform an extensive comparison between our new model and the gene teams model developed by Bergeron <it>et al</it>. As compared to the gene teams model, our new cluster model has a slightly lower recall but a higher precision at all levels of recall when the results were ranked using statistical tests. An analysis of the most significant BBH <it>r</it>-window gene cluster show that they correspond to known operons.</p

The Randomized Slicer for CVPP: Sharper, Faster, Smaller, Batchier

Following the recent line of work on solving the closest vector problem with preprocessing (CVPP) using approximate Voronoi cells, we improve upon previous results in the following ways:-We derive sharp asymptotic bounds on the success probability of the randomized slicer, by modelling the behaviour of the algorithm as a random walk on the coset of the lattice of the target vector. We thereby solve the open question left by Doulgerakis\xe2\x80\x93Laarhoven\xe2\x80\x93De Weger [PQCrypto 2019] and Laarhoven\xc2\xa0[MathCrypt 2019].-We obtain better trade-offs for CVPP and its generalisations (strictly, in certain regimes), both with and without nearest neighbour searching, as a direct result of the above sharp bounds on the success probabilities.-We show how to reduce the memory requirement of the slicer, and in particular the corresponding nearest neighbour data structures, using ideas similar to those proposed by Becker\xe2\x80\x93Gama\xe2\x80\x93Joux [Cryptology ePrint Archive, 2015]. Using 20.185d+o(d)memory, we can solve a single CVPP instance in 20.264d+o(d)time.-We further improve on the per-instance time complexities in certain memory regimes, when we are given a sufficiently large batch of CVPP problem instances for the same lattice. Using memory, we can heuristically solve CVPP instances in amortized time, for batches of size at least.Our random walk model for analysing arbitrary-step transition probabilities in complex step-wise algorithms may be of independent interest, both for deriving analytic bounds through convexity arguments, and for computing optimal paths numerically with a shortest path algorithm. As a side result we apply the same random walk model to graph-based nearest neighbour searching, where we improve upon results of Laarhoven [SOCG 2018] by deriving sharp bounds on the success probability of the corresponding greedy search procedure

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Analysis of DNA Methylation in Various Swine Tissues

DNA methylation is known to play an important role in regulating gene expression during biological development and tissue differentiation in eukaryotes. In this study, we used the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) method to assess the extent and pattern of cytosine methylation in muscle, heart, liver, spleen, lung, kidney and stomach from the swine strain Laiwu, and we also examined specific methylation patterns in the seven tissues. In total, 96,371 fragments, each representing a recognition site cleaved by either or both EcoRI + HpaII and EcoRI + MspI, the HpaII and MspI are isoschizomeric enzymes, were amplified using 16 pairs of selective primers. A total of 50,094 sites were found to be methylated at cytosines in seven tissues. The incidence of DNA methylation was approximately 53.99% in muscle, 51.24% in the heart, 50.18% in the liver, 53.31% in the spleen, 51.97% in the lung, 51.15% in the kidney and 53.39% in the stomach, as revealed by the incidence of differential digestion. Additionally, differences in DNA methylation levels imply that such variations may be related to specific gene expression during tissue differentiation, growth and development. Three types of bands were generated in the F-MSAP profile, the total numbers of these three types of bands in the seven tissues were 46,277, 24,801 and 25,293, respectively