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Nucleic Acids Research Advance Access originally published online on November 16, 2006
Nucleic Acids Research 2007 35(Database issue):D624-D629; doi:10.1093/nar/gkl833
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Nucleic Acids Research, 2007, Vol. 35, Database issue D624-D629
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

MamPol: a database of nucleotide polymorphism in the Mammalia class

Raquel Egea, Sònia Casillas, Enol Fernández1, Miquel Àngel Senar1 and Antonio Barbadilla*

Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona 08193 Bellaterra, Barcelona, Spain 1 Departament d'Arquitectura d'Ordinadors i Sistemes Operatius, Universitat Autònoma de Barcelona 08193 Bellaterra, Barcelona, Spain

*To whom correspondence should be addressed. Tel: +34 93 581 2730; Fax: +34 93 581 2387; Email: antonio.barbadilla{at}uab.es

Received July 31, 2006. Revised October 6, 2006. Accepted October 6, 2006.

Multi-locus and multi-species nucleotide diversity studies would benefit enormously from a public database encompassing high-quality haplotypic sequences with their associated genetic diversity measures. MamPol, ‘Mammalia Polymorphism Database’, is a website containing all the well-annotated polymorphic sequences available in GenBank for the Mammalia class grouped by name of organism and gene. Diversity measures of single nucleotide polymorphisms are provided for each set of haplotypic homologous sequences, including polymorphism at synonymous and non-synonymous sites, linkage disequilibrium and codon bias. Data gathering, calculation of diversity measures and daily updates are automatically performed using PDA software. The MamPol website includes several interfaces for browsing the contents of the database and making customizable comparative searches of different species or taxonomic groups. It also contains a set of tools for simple re-analysis of the available data and a statistics section that is updated daily and summarizes the contents of the database. MamPol is available at http://mampol.uab.es/ and can be downloaded via FTP.


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R. Egea, S. Casillas, and A. Barbadilla
Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W157 - W162.
[Abstract] [Full Text] [PDF]


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