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Bioinformatics Advance Access published online on February 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti326
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received September 10, 2004
Revised January 27, 2005
Accepted February 10, 2005

Applications note

MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies

Ana Tereza R. de Vasconcelos 1*, Ana Carolina R. Guimarães 1, Carlos Henrique M. Castelletti 1, Célia S. Caruso 1, Cristina Ribeiro 1, Fabiano Yokaichiya 1, Geraldo R. G. Armôa 2, Gislaine da Silva P. Pereira 1, Israel Tojal da Silva 1, Carlos G. Schrago 3, Adélia L. V. Fernandes 1, Aline R. da Silveira 1, André G. Carneiro 1, Bruno M. Carvalho 1, Carlos J. M. Viana 1, Daniel Gramkow 1, Franklin J. Lima 1, Luiz G. G. Corrêa 1, Maurício de A. Mudado 1, Pablo Nehab-Hess 3, Rangel de Souza 1, Régis L. Corrêa 1, and Claudia A. M. Russo 3

1 Laboratório Nacional de Computação Científica LNCC/MCT, Petrópolis, RJ, Brazil
2 Instituto de Bio-Manguinhos, FIOCRUZ, Rio de Janeiro, RJ, Brazil
3 UFRJ, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil

* To whom correspondence should be addressed.
Ana Tereza R. de Vasconcelos, E-mail: atrv{at}lncc.br


  Abstract

Summary: MamMibase, the Mammalian Mitochondrial Genome Database, is a relational database of complete mitochondrial genome sequences of mammalian species. The database is useful for phylogenetic analysis, since it allows a ready retrieval of nucleotide and aminoacid individual alignments, in three different formats (NEXUS for PAUP program, for MEGA program and for PHYLIP program) of the 13 protein coding mitochondrial genes. The user may download the sequences that is useful for him/her based on their parameters values, such as sequence length, p-distances, base content, transition transversion ratio, gamma, that are also given by Mammibase. A simple phylogenetic tree (neighbor-joining tree with Jukes Cantor distance) is also available for download, useful for parameter calculations and other simple tasks.

Availability: MamMiBase is available at www.mammibase.lncc.br.


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