DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus

Motivation: Polymorphism studies are one of the main research areas of this genomic era. To date, however, no comprehensive secondary databases have been designed to provide searchable collections of polymorphic sequences with their associated diversity measures. Results: We define a data model for...

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Bibliographic Details
Published inBioinformatics Vol. 21; no. suppl-2; pp. ii26 - ii30
Main Authors Casillas, Sònia, Petit, Natalia, Barbadilla, Antonio
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.09.2005
Oxford Publishing Limited (England)
Subjects
Animals
Base Sequence
Chromosome Mapping - methods
Database Management Systems
Databases, Genetic
DNA Mutational Analysis - methods
Drosophila
Drosophila - genetics
Genetic Variation - genetics
Information Storage and Retrieval - methods
Molecular Sequence Data
Polymorphism, Genetic - genetics
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Summary:Motivation: Polymorphism studies are one of the main research areas of this genomic era. To date, however, no comprehensive secondary databases have been designed to provide searchable collections of polymorphic sequences with their associated diversity measures. Results: We define a data model for the storage, representation and analysis of genotypic and haplotypic data. Under this model we have created DPDB, ‘Drosophila Polymorphism Database’, a web site that provides a daily updated repository of all well-annotated polymorphic sequences in the Drosophila genus. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity, linkage disequilibrium and codon bias. For data collection, analysis and updating we use PDA, a pipeline that automates the process of sequence retrieval, grouping, alignment and estimation of nucleotide diversity from Genbank sequences in different functional regions. The web site also includes analysis tools for sequence comparison and the estimation of genetic diversity, a page with real-time statistics of the database contents, a help section and a collection of selected links. Availability: DPDB is freely available at http://dpdb.uab.es and can be downloaded via FTP. Contact: antonio.barbadilla@uab.es
Bibliography:To whom correspondence should be addressed.
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ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bti1103