HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research

BACKGROUND: Population genetics studies based on the analysis of mtDNA and mitochondrial disease studies have produced a huge quantity of sequence data and related information. These data are at present worldwide distributed in differently organised databases and web sites not well integrated among them. Moreover it is not generally possible for the user to submit and contemporarily analyse its own data comparing them with the content of a given database, both for population genetics and mitochondrial disease data. RESULTS: HmtDB is a well-integrated web-based human mitochondrial bioinformatic resource aimed at supporting population genetics and mitochondrial disease studies, thanks to a new approach based on site-specific nucleotide and aminoacid variability estimation. HmtDB consists of a database of Human Mitochondrial Genomes, annotated with population data, and a set of bioinformatic tools, able to produce site-specific variability data and to automatically characterize newly sequenced human mitochondrial genomes. A query system for the retrieval of genomes and a web submission tool for the annotation of new genomes have been designed and will soon be implemented. The first release contains 1255 fully annotated human mitochondrial genomes. Nucleotide site-specific variability data and multialigned genomes can be downloaded. Intra-human and inter-species aminoacid variability data estimated on the 13 coding for proteins genes of the 1255 human genomes and 60 mammalian species are also available. HmtDB is freely available, upon registration, at . CONCLUSION: The HmtDB project will contribute towards completing and/or refining haplogroup classification and revealing the real pathogenic potential of mitochondrial mutations, on the basis of variability estimation

Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria

<p>Abstract</p> <p>Background</p> <p>A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinformatic surveys is due to the presence of mobile introns in almost all the fungal mitochondrial genes. The aim of this work is to verify the incidence of this phenomenon in Ascomycota, testing, at the same time, a new bioinformatic tool for extracting and managing sequence databases annotations, in order to identify the mitochondrial gene regions where introns are missing so as to propose them as species markers.</p> <p>Methods</p> <p>The general trend towards a large occurrence of introns in the mitochondrial genome of Fungi has been confirmed in Ascomycota by an extensive bioinformatic analysis, performed on all the entries concerning 11 mitochondrial protein coding genes and 2 mitochondrial rRNA (ribosomal RNA) specifying genes, belonging to this phylum, available in public nucleotide sequence databases. A new query approach has been developed to retrieve effectively introns information included in these entries.</p> <p>Results</p> <p>After comparing the new query-based approach with a blast-based procedure, with the aim of designing a faithful Ascomycota mitochondrial intron map, the first method appeared clearly the most accurate. Within this map, despite the large pervasiveness of introns, it is possible to distinguish specific regions comprised in several genes, including the full NADH dehydrogenase subunit 6 (ND6) gene, which could be considered as barcode candidates for Ascomycota due to their paucity of introns and to their length, above 400 bp, comparable to the lower end size of the length range of barcodes successfully used in animals.</p> <p>Conclusion</p> <p>The development of the new query system described here would answer the pressing requirement to improve drastically the bioinformatics support to the DNA Barcode Initiative. The large scale investigation of Ascomycota mitochondrial introns performed through this tool, allowing to exclude the introns-rich sequences from the barcode candidates exploration, could be the first step towards a mitochondrial barcoding strategy for these organisms, similar to the standard approach employed in metazoans.</p

HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research-2

<p><b>Copyright information:</b></p><p>Taken from "HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research"</p><p></p><p>BMC Bioinformatics 2005;6(Suppl 4):S4-S4.</p><p>Published online 1 Dec 2005</p><p>PMCID:PMC1866381.</p><p></p>program, three variability analyses are executed separately: nucleotide variability values for both the entire set of genomes and the continent-specific subsets are estimated through SiteVar program applied on real dataset (right hand side of the Work Flow) and on 100 simulated multialignments obtained through an automatic procedure for each continent-specific genomes dataset (in the middle of the Work Flow); aminoacid variability data (left hand side of the Work Flow) are produced by applying MitVarProt software to the 13 multialigned mitochondrial protein coding genes, automatically selected from the entire starting nucleotide multialignment and translated into aminoacid sequences through TRANSEQ program; the data produced through this three procedures are inserted in NT_VARIABILITY, NT_VARIABILITY_SIM and AA_VARIABILITY tables of the relational HmtDB structure respectively

Design of pages related to Query function as it will be implemented in the database

<p><b>Copyright information:</b></p><p>Taken from "HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research"</p><p></p><p>BMC Bioinformatics 2005;6(Suppl 4):S4-S4.</p><p>Published online 1 Dec 2005</p><p>PMCID:PMC1866381.</p><p></p> a) Multicriterion query form. b) Example of a query result