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  • 1
    Language: English
    In: BMC Genomics, Sept 15, 2008, Vol.9(414), p.414
    Description: Background The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, BLAST Output Visualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations.
    Keywords: Applications Software -- Usage ; Genetic Research -- Technology Application ; Visualization (Computer) -- Usage
    ISSN: 1471-2164
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  • 2
    Language: English
    In: BMC Genomics, London: BioMed Central Ltd.
    Description: Article discussing research on BOV, a web-based BLAST output visualization tool.
    Keywords: Output Visualization Tools ; Blast Output Visualization ; Bov ; Genomic Research
    ISSN: 14712164
    E-ISSN: 14712164
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  • 3
    Language: English
    In: IEEE INFOCOM 2008 - The 27th Conference on Computer Communications, April 2008, pp.1624-1632
    Description: Recently, wireless mesh technology has been used for military applications and fast recovery networks, referred to as nomadic wireless mesh networks (NWMNs). In such systems, wireless routers, termed nodes, are mounted on top of vehicles or vessels, which may change their location according to application needs; and the nodes are required to establish a reliable wireless mesh network. For improving network performance, some vendors use directional antennas, and the mesh topology comprises of point-to-point connections between adjacent nodes. The number of point-to-point connections of a node is upper-bounded by the number of directional radios it has, which is typically a small constant. This raises the need to build robust (i.e., two-node/edge- connected) mesh networks with bounded node degree, regardless of node locations. In this paper, we present simple elegant schemes for constructing such efficient and robust wireless mesh networks with provably small constant degree bounds. Our extensive simulations show our schemes build robust and efficient topologies for various settings with node degree bounded by 4 and small hop-count distance between nodes and gateways.
    Keywords: Robustness ; Wireless Mesh Networks ; Directional Antennas ; Peer to Peer Computing ; Marine Vehicles ; Network Topology ; Ip Networks ; Directive Antennas ; Interference ; Broadband Communication ; Engineering
    ISBN: 9781424420254
    ISBN: 1424420253
    ISSN: 0743166X
    Source: IEEE Conference Publications
    Source: IEEE Xplore
    Source: IEEE Journals & Magazines 
    Source: IEEE eBooks
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  • 4
    Language: English
    In: Computer Networks, 2008, Vol.52(9), pp.1782-1796
    Description: A radio frequency identifier (RFID) system consists of inexpensive, uniquely-identifiable tags that are mounted on physical objects, and readers that track these tags (and hence these physical objects) through RF communication. For many performance measures in large-scale RFID systems, the set of tags to be monitored needs to be properly balanced among all readers. In this paper we, therefore, address this load balancing problem for readers — how should a given set of tags be assigned to readers such that the cost for monitoring tags across the different readers is balanced, while guaranteeing that each tag is monitored by at least one reader. We first present centralized solutions to two different variants of this load balancing problem: (i) min–max cost assignment (MCA), and (ii) min–max tag count assignment (MTA). We show that MCA, the generalized variant of the load balancing problem, is NP-hard and hence present a 2-approximation algorithm for it. We next present an optimal centralized solution for MTA, an important specialized variant of the problem. Subsequently, we present a localized distributed algorithm that is probabilistic in nature and closely matches the performance of the centralized algorithms. Finally we present detailed simulation results that illustrate the performance of the localized distributed approach, how it compares with the centralized optimal and near-optimal solutions, and how it adapts the solution with changes in tag distribution and reader topology. Our results demonstrate that our schemes achieve very good performance even in highly dynamic large-scale RFID systems.
    Keywords: Rfid ; Load Balancing ; Min–Max Assignment ; Engineering
    ISSN: 1389-1286
    E-ISSN: 1872-7069
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  • 5
    Language: English
    Description: This paper discusses an ad hoc query tool for relational databases. Most Web servers hosting biological data limit users to a defined set of search options and output formats that are short of the whole range of options available to users with direct database access. However, to make full use of the wealth of data in the database resource, it is desirable to have an intermediate solution that provides a broad range of flexible query and output options through a Web portal.
    Keywords: Ad Hoc Queries ; Relational Databases
    Source: University of North Texas
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