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MBGD / Microbial Genome Database
Gathers information related to full microbial genomes. MBGD is a repository that focuses in assisting researchers in comparing genomic information by providing data about both prokaryotic and eukaryotic microbes as well as four multicellular eukaryotes. The database contains precomputed orthologs tables and permits users to generate their own. It also includes a function: MyMBGD, for submitting users’ data to the server and perform a customized ortholog analysis.
OrthoDB
Provides orthologs, genes inherited by extant species from a single gene in their last common ancestor. OrthoDB includes a total of 5756 species, providing ortholog groups for the clades of: 3663 bacteria, 330 metazoans, 227 fungi, 345 archaea and 1157 viruses. Among the metazoans, there are 172 vertebrates and 133 arthropods. There are 290 orthology levels, that were retrieved from the NCBI Taxonomy. The web resource presenting the OrthoDB data enables identified user sessions to analyze custom data sets in the context of the available orthology data, as well as to generate publication quality comparative genomics reports.
OrthoMCL-DB
forum (1)
Contains ortholog groups for most completely sequenced and annotated eukaryotes for a number of completely sequenced and annotated prokaryotes. OrthoMCL-DB provides a wealth of functionality, including domain architecture for each group, phyletic patterns for each group and advanced querying, including phylogenetic pattern searches. The database gives also access to OrthoMCL, which groups proteins into “ortholog groups” (i.e. set of proteins across one or more species that represent putative orthologs and in-paralogs).
InParanoid
Developed to address the need to identify orthologs. InParanoid uses the pairwise similarity scores, calculated using NCBI-Blast, between two complete proteomes for constructing orthology groups. An orthology group is initially composed of two so-called seed orthologs that are found by two-way best hits between two proteomes. More sequences are added to the group if there are sequences in the two proteomes that are closer to the corresponding seed ortholog than to any sequence in the other proteome. These members of an orthology group are called inparalogs. A confidence value is provided for each inparalog that shows how closely related it is to its seed ortholog.
pVOGs / prokaryotic Virus Orthologous Groups
Represents a comprehensive set of orthologous gene families shared across multiple complete genomes of viruses that infect bacterial or archaeal hosts. The uses of pVOGs include functional annotation of viral proteins, identification of genes and viruses in uncharacterized DNA samples, phylogenetic analysis and large-scale comparative genomics projects. This database provides evolutionary gene families from nearly 3000 complete genomes of viruses that infect bacteria or archaea as a pre-computed resource.
FLAGdb++
Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge.
Evola / Database of Evolutionary Features of Human Genes
Provides orthology information about originally annotated human genes in the H-Invitational database (H-InvDB). Evola contains two datasets (i) a comprehensive set of orthologs and (ii) more reliable orthologs supported by manual curation. Besides orthology information can be used with close reference to other annotation in H-InvDB. The database includes over 18 968 human genes among 11 vertebrates as well as chimpanzee, macaque, cow, or Fugu.
OPTIC / Orthologous and Paralogous TranscrIpts in Clades
Provides sets of gene predictions and orthologous groups for six clades. OPTIC is designed to provide pre-calculated phylogenetic datasets that are benefit to clade genomic analyses. A useful feature of the database is its provision of multiple alignments either for genes as concatenated exons, or for alternative transcripts. For each orthologous group, OPTIC indicates transcript predictions, orthologs, multiple alignments and phylogenetic trees.
PhenoHM
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Allows identification of genes triggering similar outcomes in human and mouse and facilitates identification of potentially novel disease causal genes. PhenoHM is a resource of human and mouse phenotype data. Users can query for genes and gene products across mouse and human based on Mammalian Phenotype Ontology (MPO) terms or disease concepts from Unified Medical Language System (UMLS) or HP terms from Human Phenotype Ontology (HPO) or Online Mendelian Inheritance in Man (OMIM) and get a mapping between the human and mouse phenotypes.
HieranoiDB
An online database for hierarchical groups of orthologs inferred by the Hieranoid algorithm. HieranoiDB with a web interface makes it easy to search and visualize the output of Hieranoid, and to download it in various formats. Searching can be performed using protein description, identifier or sequence. Orthologs are available for the 66 Quest for Orthologs reference proteomes. The ortholog trees are shown graphically and interactively with marked speciation and duplication nodes that show the inferred evolutionary scenario, and allow for correct extraction of predicted orthologs from the Hieranoid trees.
OrthoDisease
Provides a database of human disease orthologs. OrthoDisease contains 2935 distinct human disease phenotypes from OMIM, mapped to 2313 out of 21 673 human genes and their orthologs in 99 other species from InParanoid. It is possible to search for orthologs of genes involved in particular diseases, in one or all model organisms, as well as to list all disease gene ortholog groups that exist between human and a particular species. Furthermore, the web server provides gene identifier, OMIM number and free text search options. Additionally, the download view allows the user to download all disease gene ortholog groups between human and another species as a file. Each disease gene ortholog group in OrthoDisease consists of the seed ortholog pair and, possibly, a set of genes inparalogous to the seeds. For each gene in the group, an inparalog score is provided that corresponds to the certainty of its inclusion.
PGDBj / Plant Genome DataBase Japan
Provides plant genome-related information from databases (DBs) and literature. PGDBj is composed of three distinct parts: (1) the Ortholog DB, providing gene cluster information based on the amino acid sequence similarity; (2) the Plant Resource DB, supplying cDNA and genome sequence resources accumulated; and (3) the DNA Marker DB, offering manually or automatically curated information of DNA markers, quantitative trait loci and related linkage maps.
EchinoDB
A repository of orthologous transcripts from echinoderms that is searchable via keywords and sequence similarity. From transcripts we identified 749,397 clusters of orthologous loci. We have developed the information technology to manage and search the loci their annotations with respect to the Sea Urchin (Strongylocentrotus purpuratus) genome. Several users have already taken advantage of these data for spin-off projects in developmental biology, gene family studies, and neuroscience. We hope others will search EchinoDB to discover datasets relevant to a variety of additional questions in comparative biology.
POGs2 / Putative Orthologous Groups 2
Brings together functional and structural annotations for orthologous genes in a manner that simplifies cross-species comparison and functional inference. POGs2 is a database that retains the user-friendly single-page view and flexible search strategies of the original POGsDB. It offers flexible and intuitive options for queries based on gene identifier, keywords, domain names, InterPro domain identifiers, and predicted or established intracellular locations.
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