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  1. Greengenes (View Publication)
    Full Name of the Resource : Multiple sequence alignment of prokaryotic 16S rDNA
    Resource Category : Databases -> RNA -> RNA Sequence, Structure and Functions

    Brief Description : An online full-length small-subunit (SSU) rRNA gene database called 'greengenes' that keeps pace with public submissions of both archaeal and bacterial 16S rDNA sequences has been established. It addresses a number of limitations currently associated with SSU rRNA records in the public databases by providing automated chimera-screening, taxonomic placement of unclassified environmental sequences using multiple published taxonomies for each record, multiple standard alignments and uniform sequence-associated information curated from GenBank records. Manipulation of 72,918 rDNA records revealed putative chimeras in 5% (1,901 of 38,412) of environmental sequences and, surprisingly, 0.5% (201/36,643) of records derived from isolates. Greengenes also provides a suite of utensils for manipulation of sequences including an alignment tool and has been streamlined to interface with the widely used ARB program.
    Subject Area : Small Subunit rRNA gene;


    Institute/s :
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, USA.
    Address of Institute/s :
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA.
    Country : United States

    Associated Institutes :

    • Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA
    • Microbial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive Bldg 400-404, Walnut Creek, CA 94598, USA
    • Danish Genome Institute, Gustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark
    • Department of Bioinformatics, Baylor University, P.O. Box 97356, 1311 S. 5th St., Waco, TX 76798-7356, USA
    • Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 977-152, Berkeley, CA 94720, USA 6Departments of Biochemistry and Mathematics, The University of Queensland, Brisbane Qld 4072, Australia 7Department of Computer Science, Chalmers University of Technology, SE-412 96, G?teborg, Sweden

    Associated Country : USA; Denmark


    Authors/Contributors : Andersen, G.L.
    Contact Email : glandersen@lbl.gov
    Year : 2003
    Language : English

    Keywords : Archaea / classification / genetics; Bacteria / classification / genetics; Databases, Nucleic Acid / standards; Genes, rRNA; Polymerase Chain Reaction; RNA, Ribosomal, 16S / genetics; Recombination, Genetic; Reproducibility of Results; Sequence Alignment; Software