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Drosophila polymorphism database

http://dpdb.uab.es/

Description :
The Drosophila Polymorphism Database (1) is a secondary database designed to provide a collection of all the existing polymorphic sequences in the Drosophila genus grouped by name of organism and gene. 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 (2,3), 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 at synonymous and nonsynonymous 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, additional information of genes and aberrations from Flybase, and the cross-references to the Popset database. 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 is available at can be freely downloaded via FTP.

Recent develoments :
The DPDB database has been reanalyzed with the new version of PDA (3) to incorporate its improved methods for data grouping and analysis.

Aknowledgement :
Ongoing funding of DPDB is provided by the Ministerio de Educación y Ciencia grants BFU2006-08640/BMC and BES-2003-0416. Initial funding for DPDB was provided by the Ministerio de Educación y Ciencia grants DGICT-PB98-0900-C02, BMC2002-01708 and BES-2003-0416, and E-biointel.

References :
1. Casillas S., Petit N. and Barbadilla A. (2005) DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus. Bioinformatics 21: ii26-ii30.
2. Casillas S and Barbadilla A. (2004) PDA: a pipeline to explore and estimate polymorphism in large DNA databases. Nucleic Acids Res. 32: W166-W169.
3. Casillas S and Barbadilla A. (2006) PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA. Nucleic Acids Res. 34: W632-W634.

MamPol

http://mampol.uab.es/

Description :
The Mammalia Polymorphism Database (1) is a secondary database designed to provide a collection of all the existing polymorphic sequences in the Mammalia class grouped by name of organism and gene. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity. For data collection, diversity measures and updating we use PDA (2), 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 at synonymous and nonsynonymous 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 mammalian publicly available nucleotide sequences (excluding ESTs, STSs, GSSs, working draft and patents) with their annotations and references from Genbank, and the cross-references to the Popset database. The database content is daily updated, and records are assigned unique and permanent MamPol 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). 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.MamPol is available at and can be downloaded via FTP.

Recent develoments :
The MamPol website includes several interfaces for browsing the contents of the database and making customisable comparative searches of different species or taxonomic groups.

Aknowledgement :
MamPol has been funded by grants BFU2006-08640/BMC, TIN2004-03388 and BES-2003-0416 from the Ministerio de Ciencia y Tecnología, and grant 2005FI-00328 from the Generalitat de Catalunya.

References :
1. Egea R, Casillas S, Fernández E, Senar MA and Barbadilla A. (2007) MamPol: a database of nucleotide polymorphism in the Mammalia class. Nucleic Acids Res. 35: in press.
2. Casillas S and Barbadilla A. (2006) PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA. Nucleic Acids Res. 34: W632-W634.

Cytokine Gene Polymorphisms

http://www.nanea.dk/cytokinesnps/

Description :
"Cytokine Gene Polymorphism in Human Disease: on-line databases" is a collection of literature databases, providing information on human cytokine and cytokine receptor gene polymorphisms, their influence on gene expression, and on disease susceptibility or outcome. Gene polymorphisms are tabulated with hyperlinks to citation details and abstracts, MACAW nucleotide sequence alignment files, and annotated text versions of the MACAW files. The effects on expression and disease association studies have been interpreted from the original publications, and are presented and classified systematically with hyperlinks to citation details and abstracts. These databases are updated annually and provide a significant resource for immunologists, geneticists and clinicians working in this fast-developing field.

References :
Hollegaard MV, Bidwell JL. (2006) Cytokine gene polymorphism in human disease: on-line databases, Supplement 3. Genes Immun. Jun;7(4):269-276

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