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  • 1
    Language: English
    In: PLoS One, San Francisco: Public Library of Science
    Description: Article on the resequencing of Treponema pallidum ssp. pallidum strains nichols and SS14 and how the correction of sequencing errors resulted in increased separation of syphilis treponeme subclusters.
    Keywords: Treponema Pallidum Ssp. Pallidum ; Syphilis ; Genome Sequences
    ISSN: 19326203
    E-ISSN: 19326203
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  • 2
    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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  • 3
    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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  • 4
    Language: English
    In: Journal Name: Science; Journal Volume: 331; Journal Issue: 6017
    Description: This document provides supporting material related to the sequencing of the ecoresponsive genome of Daphnia pulex. This material includes information on materials and methods and supporting text, as well as supplemental figures, tables, and references. The coverage of materials and methods addresses genome sequence, assembly, and mapping to chromosomes, gene inventory, attributes of a compact genome, the origin and preservation of Daphnia pulex genes, implications of Daphnia's genome structure, evolutionary diversification of duplicated genes, functional significance of expanded gene families, and ecoresponsive genes. Supporting text covers chromosome studies, gene homology among Daphnia genomes, micro-RNA and transposable elements and the 46 Daphnia pulex opsins. 36 figures, 50 tables, 183 references.
    Keywords: Ecoresponsive Daphnia Pulex ; 59 Basic Biological Sciences Ecoresponsive Daphnia Pulex
    ISSN: 00368075
    E-ISSN: 10959203
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  • 5
    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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  • 6
    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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  • 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
    In: Genome Announcements, DC: American Society for Microbiology
    Description: This article reports the draft genome sequence of a Bacillus bacterium isolated from the microflora of Nostoc colonies grown at the Andean wetlands in northern Chile.
    Keywords: Genome ; Bacillus Bacterium ; Nostoc Colonies
    Source: University of North Texas
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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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