Paper Info
Title
DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus.
Abstract
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.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.DPDB is freely available at http://dpdb.uab.es and can be downloaded via FTP.
Year
DOI
Venue
2005
10.1093/bioinformatics/bti1103
ECCB/JBI
Keywords
Field
DocType
genetic diversity,web site,associated diversity measure,nucleotide diversity,polymorphic sequence,data model,drosophila genus,analysis tool,well-annotated polymorphic sequence,haplotypic data,data collection,polymorphism,codon bias,real time,linkage disequilibrium
Data collection,Linkage disequilibrium,Genetic diversity,Computer science,Genetic variation,Bioinformatics,Data model,GenBank,Database,Codon usage bias,Nucleotide diversity
Conference
Volume
Issue
ISSN
21 Suppl 2
2
1367-4811
Citations 
PageRank 
References 
4
0.65
10
Authors
3
Name
Order
Citations
PageRank
Sònia Casillas1266.59
Natalia Petit240.99
Antonio Barbadilla3265.91