Mitochondrial DNA (mtDNA) exhibits extraordinary genetic and physical diversity across different eukaryotic lineages and among different cell and tissue types. Despite the notable variations in structural organization, the mitochondrial genome always encodes a small number of proteins essential to the oxidative phosphorylation complex.
Deals with mitochondrial proteomics. MitoMiner is a gene-centric resource that integrates different types of subcellular localisation evidence with protein information from public resources. Searches can be made by text searches, predefined or customized queries by the use of the QueryBuilder module. It allows users to investigate mitochondrial proteins, with application in mitochondrial research, such as the ability of prioritize candidate mitochondrial disease genes.
A National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes.
Supports population genetics and mitochondrial disease studies. HmtDB hosts human mitochondrial genome sequences annotated with population and variability data, the latter being estimated through the application of the SiteVar/MitVarProt programs, based on site-specific nucleotide and aminoacid variability calculations. The annotations are manually curated thus adding value to the quality of the information provided to the end-user. Classifier tools implemented in HmtDB allow the prediction of the haplogroup for any human mitochondrial genome currently stored in HmtDB or externally submitted de novo by an end-user. Haplogroup definition is based on the Phylotree system. End-users accessing HmtDB are hence allowed to: (i) browse the database through a multi-criterion query system; (ii) analyse their own human mitochondrial sequences via the classify tool or by downloading the mt-classifier tool; (iii) download multi-alignments with reference genomes as well as variability data.
Provides access to information about plant organelles. PODB consists of six individual units; namely, the electron micrograph database, the perceptive organelles database, the organelles movie database, the organellome database, the functional analysis database and a compilation of external links to pertinent databases and homepages. The database can be useful for those who wish to explore the basics of plant organelles research.
Gathers information about peroxisomal genes. PeroxisomeDB provides a manually curated repository which aims to index peroxisomal proteins and their related molecular function, metabolic pathway and disorders, mainly from human and Saccharomyces cerevisiae. In addition, the database also includes tools for organelle’s in silico detection and for identification of novel candidate peroxisomal proteins.
A comprehensive online database of all SSRs (Simple Sequence Repeats) or STRs (Short Tandem Repeats) or Microsatellites from all sequenced Chloroplast and Mitochondrial genomes available so far across all the clades of life. SSRs are considered as important genomic elements and play a major role in the understanding the underpinnings of the evolution, linkage analysis and species discrimination. ChloroMitoSSRDB 2.0 provides a wide accessible platform for accessing the microsatellites patterns using the IMEx (Imperfect Microsatellite Extractor) and MISA and along with the primer pair information for the same. Additionally, the present version of the web-servers also allows the users to analyze the whole genome, genes and also NGS reads for the identification of the SSRs.
Provides an information resource cataloging eukaryotic proteins that are known components of an organelle or major protein complex. Organelle DB is a web-accessible relational database that presents a list of proteins organized essentially by subcellular localization and/or by organism. Users can search for proteins localized to a given organelle, subcellular structure or protein complex. The scientific visualization application Organelle View allows users to dynamically generate a visual interpretation of data from Organelle DB.
A web-based database of human whole genome and complete coding region sequences. mtDB is the only comprehensive online source for the data contained within it. This includes the sequences themselves as many have not been deposited in a publicly available database such as GenBank. The list of mitochondrial polymorphisms continually grows with the addition of new sequences and is an important resource for phylogenetic and medical studies. The ability to search for multiple-variant haplotypes adds further detail to the latent data.
Delivers an extensive repository of mtDNA data integrated with longevity records and the results of the statistical and correlative analysis of the links between them. MitoAge contains tools offering options for: (1) computation of basic statistics, (2) comparison of stats between selected taxonomic groups and (3) data export for a data set of interest. The database has permitted underling over 3780 statistically significant correlations between mtDNA features and animal longevity in different taxonomic groups.
Provides access to the published mitochondrial sequences coming from old DNA samples (aDNA). AmtDB is a database of ancient human mitochondrial genomes that offers a mapping the published aDNA samples from different sources, and supplies the associated metadata together with the mitochondrial (mt) genomes sequences and links to other resources. Samples can be browsed based on primary and alternative ID(s), geographic location descriptors, latitude and longitude, archaeological site or group of archaeological cultural background descriptors.
Deals with Mitochondrial DNA (mtDNA). EMPOP is a collaborative repository hosting information related to more than 30000 quality-controlled mitotypes including HVS-variations. Users can query data by populations using an accession number, a geographic area or a specific metapopulation. The platform also gives access to three tools allowing the retrieving of haplogroups, perform plausibility checks or compute quasi-median networks.
Consists of an online database of complete mitochondrial genome sequences of mammalian species. MamMiBase works in three steps: (1) selection of mammalian species or group; (2) selection of the outgroup from a list that included all species selected in the first stage; and (3) selection of individual mitochondrial gene alignments or a phylogenetic tree. Moreover, this repository permits users to browse and download nucleotide and protein gene sequence alignments from complete mammalian mitochondrial genomes.
Provides a phylogenetic tree of global human mitochondrial DNA (mtDNA) variation, based on both coding- and control-region mutations, and including haplogroup nomenclature. PhyloTree.org is a database which gives access to references to consulted papers as well as to accession numbers of underlying NCBI GenBank sequences. The database is meant as a framework for scientists interested in the description and application of human mtDNA diversity.
Provides precise mitogenomic annotations. MitoFish is an online resource that collects fish mitogenomic sequence data. It offers four main functions: species/taxonomy search, sequence similarity search, batch data download, and fish mitogenome annotation. For users who need more information on taxonomy, fish habitats, phenotypes, or life cycles, MitoFish provides links to related databases such as FishBase, NCBI Taxonomy, Integrated Taxonomic Information System, and the Catalog of Fishes.
Provides a collection of thirteen protein-coding and two ribosomal RNA genes sequences encoded in the mitochondrial genome. MIDORI is composed of mitochondria-related gene sequences, metazoan gene sequences and taxonomic ranking information onto each sequence. The database was constructed with nucleotide sequences from GenBank BLAST NT. It provides two different sections: Midori-UNIQUE, dedicated to unique haplotypes and Midori-LONGEST containing contains a single sequence: the longest.
A centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community. MSeqDR facilitates clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. It also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis.