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HmtDB - Human Mitochondrial DataBase


NAR Molecular Biology Database Collection entry number 1174
Rubino, Francesco; Piredda, Roberta; Calabrese, Francesco; Simone, Domenico; Lang, Martin; Calabrese, Claudia; Petruzzella, Vittoria; Tommaseo-Ponzetta, Mila; Gasparre, Giuseppe; Attimonelli, Marcella
1Università degli Studi di Bari, Dipartimento di Biochimica e Biologia Molecolare "E. Quagliariello", via Orabona n°4, 70126 Bari, Italy
2Università degli Studi di Pavia, Dipartimento di Genetica e Microbiologia, via Ferrata n°1, 27100 Pavia, Italy

Database Description

HmtDB is a well-integrated web-based human mitochondrial bioinformatics resource aimed at supporting population genetics and mitochondrial disease studies, thanks to a new approach based on site-specific nucleotide and aminoacid variability estimation (Attimonelli et al. 2005). HmtDB consists of a database of Human Mitochondrial Genomes, annotated with population data, and a set of bioinformatics tools, able to produce site-specific variability data and to automatically characterize newly sequenced human mitochondrial genomes. HmtDB is structured in five macro-functions: "Query", "Analyze your genome", "Submission", "HmtDB downloading" and "Session Query History", available from the Menu page. The Query page allows the users to draw data from HmtDB, through a multi criterion form made up of pop-up menus and free text retrieval windows. The Analyze your genome function can be used to automatically characterize a mitochondrial sequence. Through the Submission page the users can submit a new human mitochondrial genome. HmtDB downloading allows the researchers to view and download multi-aligned sequence data and site-specific nucleotide variability data, both regarding the entire database, continent specific and patient subsets. Intra-human and inter-species aminoacid variability data estimated on the 13 coding for proteins genes of the available human genomes and 60 mammalian species are also available. Thanks to the existence of Session Query History, the users can view the history of previously performed analyses. The current release of HmtDB provides access to variability and sequence data of 2879 human mitochondrial genomes from normal subjects and 609 from subjects with clinical phenotype (update September 2007). The human mitochondrial genomes in HmtDB are fully annotated with information about sample: ethnic origin, age, phenotype of the subject and tissue. HmtDB is freely available at http://www.hmdb.uniba.it. The HmtDB project has contributed to complete and/or refine human mitochondrial haplogroup classification on the basis of variability estimation. Indeed, variability the nucleotidic mitochondrial sites, presenting discriminating variability values estimated to the continent-specific datasets compared to the rest of the world, can be considered good population markers (Accetturo et al.2006). From a clinical point of view, site-specific variability values could help to understand the real pathogenic potential of mitochondrial mutations. Indeed, high nucleotidic and aminoacidic variability values inter- and intra-species are indicative of low functional constraints in the region presenting them.

Acknowledgements

This work was supported by the "Ministero Università e Ricerca Scientifica", Italy (PRIN2003; Progetto MURST Cluster C03/2000, CEGBA), MIUR - Functional Genomics and by a fund from ESF (P.O.P. 2000-2006). Accetturo M. was supported by a fellowship and fund from ESF (P.O.P. 2000–2006). We thank Prof. Antonio Torroni of the Dept. of Genetics and Microbiology of the University of Pavia, for his invaluable support and advice regarding human mtDNA haplogroup classification.

References

1. Attimonelli M, Accetturo M, Santamaria M, Lascaro D, Scioscia G, Pappadà G, Russo L, Zanchetta L, Tommaseo-Ponzetta M. (2005) HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research. BMC Bioinformatics, 6(4):S4.
2. Accetturo M, Santamaria M, Lascaro D, Rubino F, Achilli A, Torroni A, Tommaseo-Ponzetta M, Attimonelli M. (2006) Human mtDNA Site-Specific Variability Values Can Act as Haplogroup Markers. Human Mutation 27(9), 965-974.


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