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  • 1
    Language: English
    In: Current protocols in bioinformatics, March 2011, Vol.Chapter 9, pp.Unit 9.14
    Description: GBrowse is widely used by biologists to visualize genome annotation. We have developed WebGBrowse to facilitate hosting multiple GBrowse instances specific for different users on the same Web server. WebGBrowse automatically sets up each user-specific GBrowse instance by extracting information from user-supplied data to produce the appropriate configuration. This unit describes installation and administration of WebGBrowse for bioinformaticians who plan to manage local WebGBrowse servers in their institutions.
    Keywords: Molecular Sequence Annotation ; Software ; Genomics -- Methods
    ISSN: 19343396
    E-ISSN: 1934-340X
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 2
    Language: English
    In: BMC bioinformatics, 02 August 2011, Vol.12, pp.316
    Description: The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing ones allow biologists to upload their own data for analysis. We have developed the web-based Genome Synteny Viewer (GSV) that allows users to upload two data files for synteny visualization, the mandatory synteny file for specifying genomic positions of conserved regions and the optional genome annotation file. GSV presents two selected genomes in a single integrated view while still retaining the browsing flexibility necessary for exploring individual genomes. Users can browse and filter for genomic regions of interest, change the color or shape of each annotation track as well as re-order, hide or show the tracks dynamically. Additional features include downloadable images, immediate email notification and tracking of usage history. The entire GSV package is also light-weighted which enables easy local installation. GSV provides a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser. A web server hosting GSV is provided at http://cas-bioinfo.cas.unt.edu/gsv, and the software is also freely available for local installations.
    Keywords: Internet ; Software ; Synteny ; Genomics -- Methods ; Sequence Analysis, DNA -- Methods
    E-ISSN: 1471-2105
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  • 3
    Language: English
    In: Cold Spring Harbor protocols, March 2010, Vol.2010(3), pp.pdb.prot5392
    Description: Although GBrowse is popular for visualizing genomic features along a reference sequence, its installation and configuration are difficult for many biologists. WebGBrowse is a web server that takes a user-supplied annotation file, guides users to configure the display of each genomic feature, and allows users to visualize the genome annotation with integrated GBrowse software. This protocol guides the user through each step of using WebGBrowse.
    Keywords: Databases, Genetic ; Computational Biology -- Methods
    E-ISSN: 1559-6095
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  • 4
    Language: English
    In: BMC bioinformatics, 02 August 2012, Vol.13, pp.190
    Description: Web-based synteny visualization tools are important for sharing data and revealing patterns of complicated genome conservation and rearrangements. Such tools should allow biologists to upload genomic data for their own analysis. This requirement is critical because individual biologists are generating large amounts of genomic sequences that quickly overwhelm any centralized web resources to collect and display all those data. Recently, we published a web-based synteny viewer, GSV, which was designed to satisfy the above requirement. However, GSV can only compare two genomes at a given time. Extending the functionality of GSV to visualize multiple genomes is important to meet the increasing demand of the research community. We have developed a multi-Genome Synteny Viewer (mGSV). Similar to GSV, mGSV is a web-based tool that allows users to upload their own genomic data files for visualization. Multiple genomes can be presented in a single integrated view with an enhanced user interface. Users can navigate through all the selected genomes in either pairwise or multiple viewing mode to examine conserved genomic regions as well as the accompanying genome annotations. Besides serving users who manually interact with the web server, mGSV also provides Web Services for machine-to-machine communication to accept data sent by other remote resources. The entire mGSV package can also be downloaded for easy local installation. mGSV significantly enhances the original functionalities of GSV. A web server hosting mGSV is provided at http://cas-bioinfo.cas.unt.edu/mgsv.
    Keywords: Internet ; Software ; Synteny ; Genomics -- Methods
    E-ISSN: 1471-2105
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 5
    Language: English
    In: BMC Bioinformatics, 01 August 2012, Vol.13(1), p.190
    Description: Abstract Background Web-based synteny visualization tools are important for sharing data and revealing patterns of complicated genome conservation and rearrangements. Such tools should allow biologists to upload genomic data for their own analysis. This requirement is critical because individual biologists are generating large amounts of genomic sequences that quickly overwhelm any centralized web resources to collect and display all those data. Recently, we published a web-based synteny viewer, GSV, which was designed to satisfy the above requirement. However, GSV can only compare two genomes at a given time. Extending the functionality of GSV to visualize multiple genomes is important to meet the increasing demand of the research community. Results We have developed a multi-Genome Synteny Viewer (mGSV). Similar to GSV, mGSV is a web-based tool that allows users to upload their own genomic data files for visualization. Multiple genomes can be presented in a single integrated view with an enhanced user interface. Users can navigate through all the selected genomes in either pairwise or multiple viewing mode to examine conserved genomic regions as well as the accompanying genome annotations. Besides serving users who manually interact with the web server, mGSV also provides Web Services for machine-to-machine communication to accept data sent by other remote resources. The entire mGSV package can also be downloaded for easy local installation. Conclusions mGSV significantly enhances the original functionalities of GSV. A web server hosting mGSV is provided at http://cas-bioinfo.cas.unt.edu/mgsv.
    Keywords: Biology
    ISSN: 1471-2105
    E-ISSN: 1471-2105
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  • 6
    In: Bioinformatics, 2010, Vol. 26(8), pp.1122-1124
    Description: Summary: Ergatis is a flexible workflow management system for designing and executing complex bioinformatics pipelines. However, its complexity restricts its usage to only highly skilled bioinformaticians. We have developed a web-based prokaryotic genome annotation server, Integrative Services for Genomics Analysis (ISGA), which builds upon the Ergatis workflow system, integrates other dynamic analysis tools and provides intuitive web interfaces for biologists to customize and execute their own annotation pipelines. ISGA is designed to be installed at genomics core facilities and be used directly by biologists. ISGA is accessible at and the system is also freely available for local installation. 〈p〉〈bold〉Contact:〈/bold〉 〈email〉qunfeng.dong@unt.edu〈/email〉〈/p〉 are available at online.
    Keywords: Biology;
    ISSN: 1367-4803
    E-ISSN: 1460-2059
    E-ISSN: 13674811
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  • 7
    Language: English
    In: Bioinformatics (Oxford, England), 15 June 2009, Vol.25(12), pp.1550-1
    Description: The Generic Genome Browser (GBrowse) is one of the most widely used tools for visualizing genomic features along a reference sequence. However, the installation and configuration of GBrowse is not trivial for biologists. We have developed a web server, WebGBrowse that allows users to upload genome annotation in the GFF3 format, configure the display of each genomic feature by simply using a web browser and visualize the configured genomic features with the integrated GBrowse software. WebGBrowse is accessible via http://webgbrowse.cgb.indiana.edu/ and the system is also freely available for local installations.
    Keywords: Software ; Computational Biology -- Methods ; Genome -- Genetics
    ISSN: 13674803
    E-ISSN: 1367-4811
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  • 8
    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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  • 9
    In: Bioinformatics, 2009, Vol. 25(7), pp.956-957
    Description: Summary: Investigating the conservation of gene clusters across multiple genomes has become a standard practice in the era of comparative genomics. However, all existing software and databases rely heavily on pre-computation to identify homologous genes by genome-wide comparisons. Such pre-computing strategies lack accuracy and updating the data is computationally intensive. Since most molecular biologists are often interested only in a small cluster of genes, catering to this need, we have developed a web-based software system that allows users to upload a list of genes, perform dynamic search against the genomes of their choices and interactively visualize the gene cluster conservation using a novel multi-genome browser. Our approach avoids expensive genome-wide pre-computing and allows users to dynamically change the search criteria to fit their genes of interest. Our system can be customized for any genome sequences. We have applied it to both prokaryotic and eukaryotic genomes to illustrate its usability. Our software is freely available at . 〈p〉〈bold〉Contact:〈/bold〉 〈email〉dongq@indiana.edu〈/email〉〈/p〉
    Keywords: Biology;
    ISSN: 1367-4803
    E-ISSN: 1460-2059
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  • 10
    Language: English
    In: 2013 Proceedings IEEE INFOCOM, April 2013, pp.95-99
    Description: In this paper we design, implement and evaluate NameFilter, a two-stage Bloom filter-based scheme for Named Data Networking name lookup, in which the first stage determines the length of a name prefix, and the second stage looks up the prefix in a narrowed group of Bloom filters based on the results from the first stage. Moreover, we optimize the hash value calculation of name strings, as well as the data structure to store multiple Bloom filters, which significantly reduces the memory access times compared with that of non-optimized Bloom filters. We conduct extensive experiments on a commodity server to test NameFilter's throughput, memory occupation, name update as well as scalability. Evaluation results on a name prefix table with 10M entries show that our proposed scheme achieves lookup throughput of 37 million searches per second at low memory cost of only 234.27 MB, which means 12 times speedup and 77% memory savings compared to the traditional character trie structure. The results also demonstrate that NameFilter can achieve 3M per second incremental updates and exhibit good scalability to large-scale prefix tables.
    Keywords: Ip Networks ; Memory Management ; Ports (Computers) ; Throughput ; Instruction Sets ; Scalability ; Internet ; Engineering
    ISBN: 9781467359443
    ISBN: 1467359440
    ISSN: 0743166X
    Source: IEEE Conference Publications
    Source: IEEE Xplore
    Source: IEEE Journals & Magazines 
    Source: IEEE eBooks
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