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VBASE2


NAR Molecular Biology Database Collection entry number 621
Retter, I.1, Althaus, H.H.2,3, MÜnch, R.4 and MÜller, W.1
1 Department of Experimental Immunology, German Research Centre for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany
2 Institute for Genetics, University of Cologne, Weyertal 121, 50931 Cologne, Germany
3 current Address: Science+Computing, Hagellocher Weg 71-75, 72070 TÜbingen, Germany
4 Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany

Database 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.

Recent Developments

The VBASE2 dataset will be expanded soon. For mouse sequences, strain and haplotype will be assigned. We plan to expand the dataset to T cell receptor V genes and other species.

Acknowledgements

We are grateful to Rolf Huehne who set up the NGFN-BLAST service, supplying the base of the vbase2 dataset generation procedure. We also thank Miguel Nunes for continuous improvements of the DNAPLOT program. This work was funded by the German Bundesministerium fÜr Bildung und Forschung (BMBF) for the bioinformatics competence center 'Intergenomics' (grant no. 031U110A/031U210A).


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