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  • Computational Biology
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  • 1
    Language: English
    In: PLoS One, San Francisco: Public Library of Science
    Description: Article discussing the microbial communities in male first catch urine and how these are highly similar to those paired in urethral swab specimens.
    Keywords: Microbials ; Bacteria ; Urine
    ISSN: 19326203
    E-ISSN: 19326203
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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: 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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  • 4
    Language: English
    In: Plant physiology, October 2005, Vol.139(2), pp.610-8
    Description: PlantGDB (http://www.plantgdb.org/) is a database of plant molecular sequences. Expressed sequence tag (EST) sequences are assembled into contigs that represent tentative unique genes. EST contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. Tentative Gene Ontology terms are assigned to match those of the similar sequences identified. Genome survey sequences are assembled similarly. The resulting genome survey sequence contigs are matched to ESTs and conserved protein homologs to identify putative full-length open reading frame-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the exon-intron boundaries for gene structures are annotated by spliced alignment of ESTs and full-length cDNAs to their respective complete genome sequences. Unique genome browsers have been developed to present all available EST and cDNA evidence for current transcript models (for Arabidopsis, see the AtGDB site at http://www.plantgdb.org/AtGDB/; for rice, see the OsGDB site at http://www.plantgdb.org/OsGDB/). In addition, a number of bioinformatic tools have been integrated at PlantGDB that enable researchers to carry out sequence analyses on-site using both their own data and data residing within the database.
    Keywords: Databases, Genetic ; Genome, Plant ; Plants -- Genetics
    ISSN: 0032-0889
    E-ISSN: 15322548
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  • 5
    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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  • 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: Genome biology, 2006, Vol.7(11), pp.R111
    Description: The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, but the software supports inclusion of any property that can be associated with a genomic location. The xGDB distribution and user support utilities are available online at the xGDB project website, http://xgdb.sourceforge.net/.
    Keywords: Software ; Computational Biology -- Methods ; Genome -- Genetics ; Genomics -- Methods
    ISSN: 14656906
    E-ISSN: 1474-760X
    E-ISSN: 14656914
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  • 8
    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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  • 9
    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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  • 10
    Language: English
    In: Nucleic acids research, 01 January 2004, Vol.32(Database issue), pp.D354-9
    Description: PlantGDB (http://www.plantgdb.org/) is a database of molecular sequence data for all plant species with significant sequencing efforts. The database organizes EST sequences into contigs that represent tentative unique genes. Contigs are annotated and, whenever possible, linked to their respective genomic DNA. Genome sequence fragments are assembled similarly. The goal of the PlantGDB web site is to establish the basis for identifying sets of genes common to all plants or specific to particular species by integrating a number of bioinformatics tools that facilitate gene prediction and cross- species comparisons. For species with large-scale genome sequencing efforts, PlantGDB provides genome browsing capabilities that integrate all available EST and cDNA evidence for current gene models (for Arabidopsis thaliana, see the AtGDB site at http://www.plantgdb.org/AtGDB/).
    Keywords: Computational Biology ; Databases, Genetic ; Genes, Plant ; Genome, Plant
    E-ISSN: 1362-4962
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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