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      The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide

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          Abstract

          The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates information on over 1500 sequencing projects, of which 294 have been completed and the data deposited in the public databases. GOLD v.2 has been expanded to provide information related to organism properties such as phenotype, ecotype and disease. Furthermore, project relevance and availability information is now included. GOLD is available at http://www.genomesonline.org. It is also mirrored at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/

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          Metagenomics: application of genomics to uncultured microorganisms.

          Jo Handelsman (2004)
          Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na(+)(Li(+))/H(+) antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.
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            Exploring prokaryotic diversity in the genomic era

            Philip Hugenholtz (2002)
            Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced sampling bias towards four bacterial phyla - Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes - out of 35 bacterial and 18 archaeal phylum-level lineages. This bias is beginning to be rectified by the use of phylogenetically directed isolation strategies and by directly accessing microbial genomes from environmental samples.
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              Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.

              U S Ear, Nikos C. Kyrpides, A. Thalia Bernal-Mercado (2001)
              GOLD is a comprehensive resource for accessing information related to completed and ongoing genome projects world-wide. The database currently provides information on 350 genome projects, of which 48 have been completely sequenced and their analysis published. GOLD was created in 1997 and since April 2000 it has been licensed to Integrated Genomics. The database is freely available through the URL: http://igweb.integratedgenomics.com/GOLD/.
              Article 0 comments Cited 68 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (publisher-id): Nucleic Acids Research
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: 01 January 2006
                Publication date (Print): 01 January 2006
                Publication date (Electronic): 28 December 2005
                Volume: 34
                Issue: Database issue
                Pages: D332-D334
                Affiliations
                1Department of Pathology, Feinberg School of Medicine, Northwestern University Chicago, IL, USA
                2Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University Chicago, IL, USA
                3Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Heraklion, Crete, Greece
                4Microbial Ecology Program, Joint Genome Institute 2800 Mitchell Drive, Walnut Creek, CA, USA
                5Microbial Genome Analysis Program, Joint Genome Institute 2800 Mitchell Drive, Walnut Creek, CA, USA
                Author notes
                *To whom correspondence should be addressed. Tel: +1 925 296 5718; Fax: +1 925 296 5720; Email: NCKyrpides@ 123456lbl.gov
                Article
                DOI: 10.1093/nar/gkj145
                PMC ID: 1347507
                PubMed ID: 16381880
                SO-VID: b5724504-d63b-4cc2-a74f-0d17a2edda13
                Copyright © © The Author 2006. Published by Oxford University Press. All rights reserved
                License:

                The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@ 123456oxfordjournals.org

                History
                Date received : 15 September 2005
                Date revision received : 27 October 2005
                Date accepted : 27 October 2005
                Categories
                Subject: Article

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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