MamPol

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.

Webpage:
http://mampol.uab.es/

Tags:

human and other vertebrate genomes model organisms

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