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Nucleic Acids Research, 2000, Vol. 28, No. 1 356-360
© 2000 Oxford University Press

HGBASE: a database of SNPs and other variations in and around human genes

Anthony J. Brookes1,*, Heikki Lehväslaiho2, Marianne Siegfried1,3, Jana G. Boehm3, Yan P. Yuan4, Chandra M. Sarkar3, Peer Bork4 and Flavio Ortigao3

1Center for Genomics Research, Karolinska Institute, Theorells väg 3, S-171 77 Stockholm, Sweden, 2European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK, 3Interactiva Biotechnologie GmbH, Sedanstrasse 10, D-89077 Ulm, Germany and 4European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany

Human genome polymorphism is expected to play a key role in defining the etiologic basis of phenotypic differences between individuals in aspects such as drug responses and common disease predisposition. Relevant functional DNA changes will probably be located in or near to transcribed sequences, and include many single nucleotide polymorphisms. To aid the future analysis of such genome variation, HGBASE (Human Genic Bi-Allelic SEquences) was constructed as a means to gather human gene-linked polymorphisms from all possible public sources, and show these as a non-redundant set of records in a standardized and user-friendly database endowed with text and sequence based search facilities. After 1 year of presence on the WWW, the HGBASE project has compiled data for over 22 000 records, and this number continues to triple every 6–12 months with data harvested or submitted from all major public genome databases and published literature from the previous decade. Extensive annotation enhancement, internal consistency checking and manual review of every record is undertaken to address potential errors and deficiencies sometimes present in the original source data. The fully polished and comprehensive database is made freely available to all at http://hgbase.cgr.ki.se

* To whom correspondence should be addressed. Tel: +46 8 7286630; Fax: +46 8 331547; Email: anthony.brookes@cgr.ki.se


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