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MamPol


NAR Molecular Biology Database Collection entry number 952
Egea R.1, Casillas S.1, Fernández E.2, Senar MA.2 and Barbadilla A.1
1Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
2Departament d'Arquitectura d'Ordinadors i Sistemes Operatius, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain

Database 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 Developments

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

Acknowledgements

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.


Go to the abstract in the NAR 2007 Database Issue.
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