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  • 1
    Language: English
    In: BMC Bioinformatics, August 2, 2011, Vol.12, p.316
    Description: Background 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. Results 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. Conclusions 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: Applications Software -- Usage ; Computational Biology -- Usage ; Gene Expression -- Research ; Dna Sequencing -- Usage
    ISSN: 1471-2105
    Source: Cengage Learning, Inc.
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  • 2
    Language: English
    In: BMC Bioinformatics, August 2, 2011, Vol.12, p.316
    Description: Background 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. Results 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. Conclusions 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: Applications Software -- Usage ; Computational Biology -- Usage ; Gene Expression -- Research ; Dna Sequencing -- Usage
    ISSN: 1471-2105
    Source: Cengage Learning, Inc.
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  • 3
    Language: English
    In: PLoS One, San Francisco: Public Library of Science
    Description: Article discussing research on characteristic male urine microbiomes associated with asymptomatic sexually transmitted infection.
    Keywords: Microbiomes ; Infections ; Bacteria ; Urine
    ISSN: 19326203
    E-ISSN: 19326203
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  • 4
    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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  • 5
    Language: English
    In: BMC Bioinformatics, 01 August 2011, Vol.12(1), p.316
    Description: Abstract Background 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. Results 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. Conclusions 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: Biology
    ISSN: 1471-2105
    E-ISSN: 1471-2105
    Source: Directory of Open Access Journals (DOAJ)
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  • 6
    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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  • 7
    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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  • 8
    Language: English
    In: BMC Bioinformatics, London: BioMed Central
    Description: This article discusses a web-based multi-genome synteny viewer for customized data.
    Keywords: Genomes ; Centralized Web Resources ; Multi-Genome Synteny Viewer ; Mgsv
    Source: University of North Texas
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  • 9
    Language: English
    In: BMC Informatics, London: BioMed Central Ltd.
    Description: Article discussing the genome synteny viewer (GSV), a web-based viewer providing a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser.
    Keywords: Genomics ; Genome Synteny Viewers ; Gsv
    Source: University of North Texas
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  • 10
    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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