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A freely accessible mitochondrial proteomics database. MitoMiner integrates different types of subcellular localisation evidence with protein information from public resources, and so provides a comprehensive central resource for data on mitochondrial protein localisation. Here we report important updates to the database including the addition of subcellular immunofluorescent staining results from the Human Protein Atlas, computational predictions of mitochondrial targeting sequences, and additional large-scale mass-spectrometry and GFP tagging data sets. This evidence is shared across the 12 species in MitoMiner (now including Schizosaccharomyces pombe) by homology mapping. MitoMiner provides multiple ways of querying the data including simple text searches, predefined queries and custom queries created using the interactive QueryBuilder. For remote programmatic access, API's are available for several programming languages. This combination of data and flexible querying makes MitoMiner a unique platform to investigate mitochondrial proteins, with application in mitochondrial research and prioritising candidate mitochondrial disease genes.
mtDB / Human Mitochondrial Genome Database
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.
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.
Organelle DB
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.
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.
MitoFish / Mitochondrial Genome Database of Fish
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.
MSeqDR / the Mitochondrial Disease Sequence Data Resource Consortium
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.
Provides information about perfect, imperfect and compound Simple Sequence Repeats (SSRs). MitoSatPlant is an online resource of plant mitochondrial SSRs (mtSSRs). Additionally, Polymerase Chain Reaction (PCR) primers, statistical information such as density, average length of SSRs, frequencies of repeat type are also available. User can freely download the data available in this database which will help researchers to screen polymorphic markers in plant mitochondrial DNA.
FMGP / Fungal Mitochondrial Genome Project
Provides complete sequences mitochondrial genomes from all major fungal lineages. FMGP was developed to define the origin of the fungi, their protistan ancestors, and their specific phylogenetic link to the animals. It also permits researchers to investigate mitochondrial gene expression, introns, RNAse P RNA structures or mobile elements. This resource includes choanoflagellate protists that are believed to have evolved close to the animal/fungal divergence.
FMiR / Fish Mitogenome Resource
A database of curated fish mitochondrial sequences and presently covers mitogenome information of 1302 globally distributed fish species belonging to 297 families and 47 orders reported from saltwater and freshwater ecosystems. FMiR also contains other valuable information on each fish species such as habitat, distribution, occurrence, conservation status and taxonomy. FMiR is the workbench for finding SSR motifs, repeat orientation, sequence similarity search and annotation, identification of repeats loci and primer design. In addition, the database presents the relative abundance of microsatellite repeats in the mitogenomes. It is also possible to compare complete and individual components of genomes for deducing variation across fish species.
An integrated platform providing high quality protein-protein interaction (PPI) data in human mitochondrion and useful tools to analysis PPI network. Currently there are 490 proteins locating in mitochondrion and 2323 proteins outside mitochondrion that exist in the mitochondrial PPI network. There are totally 5883 non-redundant interactions in the database. Among them, 1640 interactions are new that have not been covered in other PPI databases such as HPRD, BioGrid, DIP and IntAct.
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