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  1. VBASE2 (View Publication)
    Full Name of the Resource : Variable genes from the Ig loci of human and mouse
    Resource Category : Databases -> Immunological Databases -> Immunological Databases

    Brief Description : VBASE2 is an integrative database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences from the EMBL database and Ensembl together with the corresponding links to the source data. The VBASE2 dataset is generated in an automatic process based on a BLAST search of V genes against EMBL and the Ensembl dataset. The BLAST hits are evaluated with the DNAPLOT program, which allows immunoglobulin sequence alignment and comparison, RSS recognition and analysis of the V(D)J-rearrangements. As a result of the BLAST hit evaluation the VBASE2 entries are classified into 3 different classes: class 1 holds sequences for which a genomic reference and a rearranged sequence is known. Class 2 contains sequences which have not been found in a rearrangement, thus lacking evidence of functionality. Class 3 contains sequences which have been found in different V(D)J rearrangements but lack a genomic reference. All VBASE2 sequences are compared with the datasets from the VBASE-, IMGT- and KABAT-databases (latest published versions), and the respective references are provided in each VBASE2 sequence entry. The VBASE2 database can be accessed by either a text based query form or by a sequence alignment with the DNAPLOT program. A DAS-server shows the VBASE2 dataset within the Ensembl Genome Browser and links to the database.

    Institute/s :
    Department of Experimental Immunology, German Research Centre for Biotechnology, Mascheroder Weg 1, Braunschweig, Germany
    Address of Institute/s :
    Department of Experimental Immunology, German Research Centre for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany
    Country : Germany

    Associated Institutes :

    • Department of Experimental Immunology, German Research Centre for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany
    • Institute for Genetics, University of Cologne, Weyertal 121, 50931 Cologne, Germany
    • Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany

    Associated Country : Germany


    Authors/Contributors : I. Retter; H.H. Althaus; R. Munch; W. Muller
    Contact Email : ida.retter@gbf.de
    Year : 2004
    Language : English

    Keywords : Animals; Databases, Nucleic Acid; Genes, Immunoglobulin; Humans; Immunoglobulin Variable Region / genetics; Mice; Systems Integration; User-Computer Interface