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Mammalia Polymorphism Database (MamPol)  

Mammalia Polymorphism Database, is a secondary database designed to provide a collection of all the existing polymorphic sequences in the Mammalia group. 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 (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 mammalian 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), and the cross-references to the PopSet database (from NCBI). 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. The database can be freely downloaded from our server.

MamPol has been created and is curated by Raquel Egea, 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). Parallelisation for database building was automated using Condor by Enol FernŠndez and Miquel ņngel Senar from the Dpt. of Computer Architecture and Operating Systems of the Universitat AutÚnoma de Barcelona (Spain). For any question about this site, please contact us.

The Mammalia Polymorphism Database (MamPol) is published in Nucleic Acids Research, volume 35 (Database issue). See abstract.

 

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