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Development of a universal, flexible and freely available database management system for gene-centered data collection, curation and display of DNA variation

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8 Author(s)
Zaimidou, S. ; MGC-Dept. of Cell, Erasmus Univ. Med. Center, Rotterdam ; van Baal, S. ; Smith, T.D. ; Mitropoulos, K.
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We report the development of a flexible database management system, based on a relational database format, for locus-specific database development and curation and its implementation for the development of a new locus-specific database, namely A1ATVar, for SERPINA1 gene variants, leading to alpha1-antitrypsin deficiency (available from http://www.goldenhelix.org/a1atvar). This tool allows data entry and display of mutation summaries in a tabular format, while user-generated queries can be formulated based on fields in the database table. A separate module, linked to FINDbase database for frequencies of inherited disorders allows the user to access relevant allele frequency information in different populations worldwide. Available experimental protocols to detect variant alleles at the protein and DNA levels can also be archived in a searchable format. A visualization tool, called VariVis, is implemented to combine variant information with gene sequence and annotation data. Finally, a direct data submission tool allows registered users to submit data on novel variant alleles as well as experimental protocols via a password-protected interface. Implementation of this tool is free of charge and there are no registration requirements for data querying. This database management system can serve as an example for an all-in-one solution for locus-specific database development and curation.

Published in:

BioInformatics and BioEngineering, 2008. BIBE 2008. 8th IEEE International Conference on

Date of Conference:

8-10 Oct. 2008

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