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Drosophila Polymorphism Database (DPDB)
Drosophila Polymorphism Database, is a secondary database designed to provide a collection of all the existing polymorphic sequences in the Drosophila genus. It allows, for the first time, the search for any polymorphic set according to different parameter values of nucleotide diversity. For data collection, diversity measures and updating we use PDA (Casillas & Barbadilla 2004, Casillas & Barbadilla 2006), a pipeline made of a set of Perl modules that automates the process of sequence retrieving, grouping, aligning and estimating diversity parameters from GenBank sequences.
Diversity measures, including polymorphism estimates in synonymous and non-synonymous sites, linkage disequilibrium and codon bias, are calculated for each polymorphic set in different functional regions. The database also includes the primary information retrieved from different external sources: the Drosophila publicly available nucleotide sequences (excluding ESTs, STSs, GSSs, working draft and patents) with their annotations and references from GenBank (see the NCBI's Disclaimer and Copyright), additional information of genes and aberrations (from FlyBase), and the cross-references to the PopSet database (from NCBI). The database content is daily updated, and records are assigned unique and permanent DPDB identification numbers to facilitate cross-database referencing.
Online query interfaces facilitate data interrogation by different polymorphism parameter values and keyword queries (based on SQL searches) and sequence similarity (with Blast). Full reports, sequences and alignments in different formats and polymorphism parameters can be obtained in both textual and graphical formats. The web site also includes software facilities for data analysis and a daily-updated web page with exhaustive statistics on the contents of the database. The database can be freely downloaded from our server.
DPDB has been funded by the Ministerio de Ciencia y TecnologŪa (DGICT-PB98-0900-C02, BMC2002-01708 and BES-2003-0416) and the bioinformatics company Ebiointel.
DPDB has been created and is curated by SÚnia Casillas and Antonio Barbadilla, from the Genomics, Bioinformatics and Evolution Research Group of the Dpt. of Genetics and Microbiology of the Universitat AutÚnoma de Barcelona (Spain). For any question about this site, please contact us.
The Drosophila Polymorphism Database (DPDB)
is listed with Accession No. 774 in the NAR Molecular
Biology Database compilation (Galperin
Nucleic Acids Res. 2005); see the recent summary at
http://www3.oup.co.uk/nar/database/summary/774. It has also been
cited in a recent review about research resources for Drosophila
in Nature Reviews Genetics (Matthews,
K.A., Kaufman, T.C and Gelbart, W.M. Nature Reviews Genetics
2005). It was officially presented at the ECCB/JBI 2005
conference in Madrid (Spain) (http://www.eccb05.org/).
Please cite this reference for
results obtained with DPDB:
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