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  1. HmtDB - Human Mitochondrial DataBase (View Publication)
    Full Name of the Resource : Human mitochondrial database
    Resource Category : Databases -> Organelle Databases -> Mitochondrial Genes and Proteins

    Brief 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.

    Institute/s :
    Universita degli Studi di Bari, Dipartimento di Biochimica e Biologia Molecolare ''E. Quagliariello'', via Orabona n*4, 70126 Bari, Italy
    Address of Institute/s :
    Universita degli Studi di Bari, Dipartimento di Biochimica e Biologia Molecolare ''E. Quagliariello'', via Orabona n*4, 70126 Bari, Italy
    Country : Italy

    Associated Institutes :

    • Universita degli Studi di Bari, Dipartimento di Biochimica e Biologia Molecolare ''E. Quagliariello'', via Orabona n*4, 70126 Bari, Italy
    • Java Technology Center, IBM Semea Sud, Via Tridente 42/14, 70125 Bari, Italy
    • Dipartimento di Zoologia, Universit√† di Bari, Via E. Orabona 4, 70126 Bari, Italy

    Associated Country : Italy


    Authors/Contributors : Attimonelli M.
    Contact Email : m.attimonelli@biologia.uniba.it
    Year : 2005
    Language : English

    Keywords : Computational Biology / *methods; *DNA, Mitochondrial; Databases, Factual; *Databases, Genetic; Databases, Nucleic Acid; Databases, Protein; Genetics, Population; Genome; Genotype; Humans; Information Storage and Retrieval; Internet; Mitochondrial Proteins / *genetics / physiology; Sequence Alignment