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Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from Contact: sa4@sanger.ac.uk PMID:19497936
Visualization is indispensable in the research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to visualize automatically the topological architectures and facilitate the understanding of the functions of the networks. We propose a novel layout algorithm to draw complex biochemical networks. A network is modeled as a system of interacting nodes on squared grids. A discrete cost function between each node pair is designed based on the topological relation and the geometric positions of the two nodes. The layouts are produced by minimizing the total cost. We design a fast algorithm to minimize the discrete cost function, by which candidate layouts can be produced efficiently. A simulated annealing procedure is used to choose better candidates. Our algorithm demonstrates its ability to exhibit cluster structures clearly in relatively compact layout areas without any prior knowledge. We developed Windows software to implement the algorithm for CADLIVE. All materials can be freely downloaded from _layout.htm; _layout.htm;
We describe an image analysis supervised learning algorithm that can automatically classify galaxy images. The algorithm is first trained using a manually classified images of elliptical, spiral, and edge-on galaxies. A large set of image features is extracted from each image, and the most informative features are selected using Fisher scores. Test images can then be classified using a simple Weighted Nearest Neighbor rule such that the Fisher scores are used as the feature weights. Experimental results show that galaxy images from Galaxy Zoo can be classified automatically to spiral, elliptical and edge-on galaxies with accuracy of 90% compared to classifications carried out by the author. Full compilable source code of the algorithm is available for free download, and its general-purpose nature makes it suitable for other uses that involve automatic image analysis of celestial objects. PMID:20161594
We have developed, applied and validated a novel algorithm called PathfinderTURB for the automatic and real-time detection of the vertical structure of the planetary boundary layer. The algorithm has been applied to a year of data measured by the automatic LIDAR CHM15K at two sites in Switzerland: the rural site of Payerne (MeteoSwiss station, 491 m, asl), and the alpine site of Kleine Scheidegg (KSE, 2061 m, asl). PathfinderTURB is a gradient-based layer detection algorithm, which in addition makes use of the atmospheric variability to detect the turbulent transition zone that separates two low-turbulence regions, one characterized by homogeneous mixing (convective layer) and one above characterized by free tropospheric conditions. The PathfinderTURB retrieval of the vertical structure of the Local (5-10 km, horizontal scale) Convective Boundary Layer (LCBL) has been validated at Payerne using two established reference methods. The first reference consists of four independent human-expert manual detections of the LCBL height over the year 2014. The second reference consists of the values of LCBL height calculated using the bulk Richardson number method based on co-located radio sounding data for the same year 2014. Based on the excellent agreement with the two reference methods at Payerne, we decided to apply PathfinderTURB to the complex-terrain conditions at KSE during 2014. The LCBL height retrievals are obtained by tilting the CHM15K at an angle of 19 degrees with respect to the horizontal and aiming directly at the Sphinx Observatory (3580 m, asl) on the Jungfraujoch. This setup of the CHM15K and the processing of the data done by the PathfinderTURB allows to disentangle the long-transport from the local origin of gases and particles measured by the in-situ instrumentation at the Sphinx Observatory. The KSE measurements showed that the relation amongst the LCBL height, the aerosol layers above the LCBL top and the gas + particle concentration is all but 2ff7e9595c
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