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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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IMG Resource Report Resource Website 500+ mentions |
IMG (RRID:SCR_007733) | IMG | data or information resource, database | Datasets and tools for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context. Plasmids that are not part of a specific microbial genome sequencing project and phage genomes are also included in order to increase its genomic context for comparative analysis. The user interface (see User Interface Map) allows navigating the microbial genome data space along its three key dimensions (genes, genomes, and functions), and groups together the main comparative analysis tools. Microbial genome data analysis in IMG usually starts with the definition of an analysis context in terms of selected genomes, functional annotations, and/or genes, followed by the individual or comparative analysis of genomes, functional annotations, or genes. | genome, microorganism, annotation, bio.tools, FASEB list |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: DOE Joint Genome Institute |
nif-0000-03009, biotools:img | https://bio.tools/img | SCR_007733 | Integrated Microbial Genomes | 2026-09-05 06:31:44 | 715 | |||||||
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LEGER: the post-genome Database for Listeria Research Resource Report Resource Website 1+ mentions |
LEGER: the post-genome Database for Listeria Research (RRID:SCR_007760) | data or information resource, database | Knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species.Provides information on gene functions (as annotated or supposed by literature from homologous organisms) , protein expression levels under defined experimental conditions ,subcellular localization of proteins (expected and/or experimentally validated) , biological meaning of genes and proteins based on KEGG, InterPro and Gene Ontology. | Proteome, functional, genome, data, protein, expression, subcellular, localization | German Bundesministerium für Bildung und Forschung (BMBF) | PMID:16381897 | Free, Freely available | nif-0000-03077 | SCR_007760 | Proteome Database LEGER | 2026-09-05 06:31:44 | 2 | |||||||
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PhylomeDB Resource Report Resource Website 50+ mentions |
PhylomeDB (RRID:SCR_007850) | data or information resource, database | Database for phylomes, that is, complete collections of phylogenetic trees for all proteins encoded in a given genome. It aims at providing a repository of high-quality phylogenies and alignments for proteins encoded in model species. To derive a phylome, each protein encoded in a given genome is used as a seed to retrieve its homologs in other complete genomes. These sequences are aligned and processed to derive reliable phylogenies using several phylogenetic methods. Besides providing the evolutionary history of the gene families, phylomeDB includes phylogeny based predictions of orthology and paralogy relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Genome-wide collections, gene phylogenies, phylogenetic trees collection, proteins encoded, genome, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:17962297 PMID:21075798 PMID:24275491 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03281, biotools:PhylomeDb | https://bio.tools/PhylomeDB | SCR_007850 | PhylomeDB | 2026-09-05 06:31:46 | 52 | ||||||
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Silkworm Genome Database Resource Report Resource Website 1+ mentions |
Silkworm Genome Database (RRID:SCR_008242) | data or information resource, database | Silkbase''s objective is to build a foundation for the complete genome analysis of Bombyx mori. | anopheles gambiae, bombyx mori, drosophila, genome, moth, samia cynthia invertebrate databases | has parent organization: University of Tokyo; Tokyo; Japan | nif-0000-21370 | SCR_008242 | Silkworm Genome Database | 2026-09-05 06:31:51 | 3 | |||||||||
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Cytokine Family Database Resource Report Resource Website 1+ mentions |
Cytokine Family Database (RRID:SCR_008134) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. A collection of cDNA, gene and protein records of cytokines deposited in public databases provides various information about the cytokine members of vertebrates in other databases including NCBI GenBank, Swiss-Prot, UniGene, TIGR (The Institute for Genomic Research) Gene Indices, Ensembl, Entrez Gene, Mouse Genome Informatics (MGI) and Rat Genome Database (RGD). It also provides orthologous relationship of cytokine members and includes novel members identified in the databases. | family, fish, gene, amphibian, bird, cdna, chemokine, cow, cytokine, genome, human, mammalian, mouse, oncogene, phylogenetic, protein, rat, receptor, reptile, virus |
is listed by: 3DVC has parent organization: Kumamoto University; Kumamoto; Japan |
Japan Society for the Promotion of Science | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20948 | http://cytokine.medic.kumamoto-u.ac.jp/ | SCR_008134 | dbCFC | 2026-09-05 06:31:50 | 1 | ||||||
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Animal Genome Database Resource Report Resource Website 1+ mentions |
Animal Genome Database (RRID:SCR_008165) | data or information resource, database | Database of comparative gene mapping between species to assist the mapping of the genes related to phenotypic traits in livestock. The linkage maps, cytogenetic maps, polymerase chain reaction primers of pig, cattle, mouse and human, and their references have been included in the database, and the correspondence among species have been stipulated in the database. AGP is an animal genome database developed on a Unix workstation and maintained by a relational database management system. It is a joint project of National Institute of Agrobiological Sciences (NIAS) and Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF-Institute), under cooperation with other related research institutes. AGP also contains the Pig Expression Data Explorer (PEDE), a database of porcine EST collections derived from full-length cDNA libraries and full-length sequences of the cDNA clones picked from the EST collection. The EST sequences have been clustered and assembled, and their similarity to sequences in RefSeq, and UniGene determined. The PEDE database system was constructed to store sequences and similarity data of swine full-length cDNA libraries and to make them available to users. It provides interfaces for keyword and ID searches of BLAST results and enables users to obtain sequence data and names of clones of interest. Putative SNPs in EST assemblies have been classified according to breed specificity and their effect on coding amino acids, and the assemblies are equipped with an SNP search interface. The database contains porcine nucleotide sequences and cDNA clones that are ready for analyses such as expression in mammalian cells, because of their high likelihood of containing full-length CDS. PEDE will be useful for researchers who want to explore genes that may be responsible for traits such as disease susceptibility. The database also offers information regarding major and minor porcine-specific antigens, which might be investigated in regard to the use of pigs as models in various medical research applications. | est, expression, gene, amino acid, animal, antigen, breed, cattle, cdna, cell, chain, clone, coding, cytogenetic, genome, human, linkage, livestock, mammalian, map, mouse, nucleotide, organism, phenotypic, pig, polymerase, porcine, primer, reaction, sequence, snp, specie, swine, trait | has parent organization: National Institute of Agrobiological Sciences; Ibaraki; Japan | nif-0000-21029 | SCR_008165 | AGP | 2026-09-05 06:31:50 | 1 | |||||||||
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Phylogenetic Clusters of Orthologous Groups Ranking Resource Report Resource Website 1+ mentions |
Phylogenetic Clusters of Orthologous Groups Ranking (RRID:SCR_008223) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 20,2019.The COG-database has become a powerful tool in the field of comparative genomics. The construction of this data-base is based on sequence homologies of proteins from different completely sequenced genomes. Highly homologous proteins are assigned to clusters of orthologous groups. The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies. The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Here is a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or approximately 54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of approximately 20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (approximately 1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes. | elegans, encephalitozoon, eukaryote, evolutionary, fly, fruit, fungus, gene, general genomics databases, animal, arabidopsis, caenorhabditis, cerevisiae, classification, comparative, cuniculi, drosophila, genome, genomic, homo, homology, intracellular, melanogaster, microsporidian, nematode, organism, ortholog, orthologous, parasite, pattern, phyletic, phylogenetic, plant, pombe, prokaryote, protein, saccharomyces, sapiens, schizosaccharomyces, sequence, thaliana, tool, unicellular | has parent organization: National Institutes of Health | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21313 | SCR_008223 | PCOGR | 2026-09-05 06:31:51 | 3 | ||||||||
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Comparative Vertebrate Sequencing Resource Report Resource Website |
Comparative Vertebrate Sequencing (RRID:SCR_008213) | data or information resource, database | Generates data for use in developing and refining computational tools for comparing genomic sequence from multiple species. The NISC Comparative Sequencing Program's goal is to establish a data resource consisting of sequences for the same set of targeted genomic regions derived from multiple animal species. The broader program includes plans for a diverse set of analytical studies using the generated sequence and the publication of a series of papers describing the results of those analysis in peer-reviewed journals in a timely fashion. Experimentally, this project involves the shotgun sequencing of mapped BAC clones. For each BAC, an assembly is first performed when a sufficient number of sequence reads have been generated to provide full shotgun coverage of the clone. At that time, the assembled sequence is submitted to the HTGS division of GenBank. Subsequent refinements of the sequence, including the generation of higher-accuracy finished sequence, results in the updating of the sequence record in GenBank. By immediately submitting our BAC-derived sequences to GenBank, it makes their data available as a public service to allow colleagues to speed up their research, consistent with the now well-established routine of sequencing centers participating in the Human Genome Project. However, at the same time, it has made considerable investment in acquiring these mapping and sequence data, including sizable efforts of graduate students, postdoctoral fellows, and other trainees. Furthermore, in most cases, large data sets involving multiple BAC sequences from multiple species must first be generated, often taking many months to accumulate, before the planned analysis can be performed and the resulting papers written and submitted for publication. | accuracy, animal, bac, clone, comparative, computational, genome, genomic, human, map, mapping, model organisms and comparative genomics databases, sequence, specie, tool | has parent organization: National Institutes of Health | nif-0000-21291 | SCR_008213 | Comparative Vertebrate Sequencing | 2026-09-05 06:31:51 | 0 | |||||||||
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Peroxisome Database Resource Report Resource Website 10+ mentions |
Peroxisome Database (RRID:SCR_008352) | data or information resource, database | The aim of the PEROXISOME database (PeroxisomeDB) is to gather, organize and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders. PeroxisomeDB contains the complete peroxisomal proteome of Homo sapiens (encoded by 85 genes) and Saccharomyces cerevisiae (encoded by 61 genes). Now, we have included 34 new organism genomes with the acquisition of 2426 new peroxisomal homolog proteins. PeroxisomeDB 2.0 integrates the peroxisomal metabolome of whole microbody family by the new incorporation of the glycosome proteomes of trypanosomatids and the glyoxysome proteome of Arabidopsis thaliana. The site also provides a Peroxisome Metabolome of peroxisomal genes and proteins, their molecular interactions and metabolic pathways, tools for comparative genomics, predictive tools. Sponsors: Preoxisome Database is funded by Institut de Gntique et deBiologie Molculaire et Cellulaire. | family, function, gene, arabidopsis thaliana, disorder, genome, genomic, glycosome, glyoxysome, homolog, homo sapiens, interaction, metabolic, metabolome, microbody, molecular, organism, pathway, peroxisome, protein, proteome, saccharomyces cerevisiae, trypanosomatid | nif-0000-25216 | SCR_008352 | Preoxisomedb | 2026-09-05 06:31:52 | 31 | ||||||||||
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Structure modeling of 907 G protein coupled receptors in the human genome Resource Report Resource Website 1+ mentions |
Structure modeling of 907 G protein coupled receptors in the human genome (RRID:SCR_008351) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19,2019.Database of tertiary structural modeling results of threading assembly refinement (TASSER) method for all 907 G protein-coupled receptors (GPCRs) in human genome. All sequences were collected from GPCR database http://www.gpcr.org/7tm/ and http://www.expasy.org/cgi-bin/lists?7tmrlist.txt. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. G protein-coupled receptors (GPCRs), encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction of endogenous signal into a cellular response. Although tertiary structural information is crucial for function annotation and drug design, there are few experimentally determined GPCR structures. To address this issue, we employ the recently developed threading assembly refinement (TASSER) method to generate structure predictions for all 907 putative GPCRs in the human genome. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. These features are essential for the comprehensive modeling of all human GPCRs when close homologous templates are absent. Based on a benchmarked confidence score, approximately 820 predicted models should have the correct folds. The majority of GPCR models share the characteristic seven-transmembrane helix topology, but 45 ORFs are predicted to have different structures. This is due to GPCR fragments that are predominantly from extracellular or intracellular domains as well as database annotation errors. Our preliminary validation includes the automated modeling of bovine rhodopsin, the only solved GPCR in the Protein Data Bank. With homologous templates excluded, the final model built by TASSER has a global C(alpha) root-mean-squared deviation from native of 4.6 angstroms, with a root-mean-squared deviation in the transmembrane helix region of 2.1 angstroms. Models of several representative GPCRs are compared with mutagenesis and affinity labeling data, and consistent agreement is demonstrated. Structure clustering of the predicted models shows that GPCRs with similar structures tend to belong to a similar functional class even when their sequences are diverse. These results demonstrate the usefulness and robustness of the in silico models for GPCR functional analysis. Sponsors: GPCR is funded by the University at Buffalo, Buffalo, New York. | endogenous, extracellular, family, functional, gene, cellular, couple, genome, gpcr, g protein, helix, homology, human, membrane, model, modeling, orf, protein, receptor, response, signal, structural, structural model, structure, template, tertiary, topology, transduction, transmembrane | has parent organization: Georgia Institute of Technology; Georgia; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25215 | SCR_008351 | GPCR | 2026-09-05 06:31:52 | 3 | ||||||||
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Metagenomics Program at JGI Resource Report Resource Website 1+ mentions |
Metagenomics Program at JGI (RRID:SCR_008804) | JGI Metagenomics Program | data or information resource, database | Portal providing access to metagenomics projects, data and tools supported by the DOE Joint Genome Institute (JGI). A primary motivation for metagenomics is that most microbes found in nature exist in complex, interdependent communities and cannot readily be grown in isolation in the laboratory. One can, however, isolate DNA or RNA from the community as a whole, and studies of such communities have revealed a diversity of microbes far beyond those found in culture collections. It is suspected that these uncultivated organisms must harbor considerable as-yet undiscovered genomic, functional, and metabolic features and capabilities. Thus to fully explore microbial genomics, it is imperative that we access the genomes of these elusive players. | genome, comparative analysis, metagenome, microbial, environment, terrestrial, aquatic, marine, freshwater, engineered, thermal spring, soil, host-associated, sequence, gene |
is listed by: 3DVC has parent organization: DOE Joint Genome Institute |
DOE | nlx_144368 | SCR_008804 | 2026-09-05 06:31:54 | 1 | ||||||||
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Ensembl Fungi Resource Report Resource Website 100+ mentions |
Ensembl Fungi (RRID:SCR_008681) | data or information resource, database | The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Fungi, which houses fungal species. Sponsors: EnsembFungi is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute. | fungus, database, genome, software, specie, taxonomic, FASEB list | has parent organization: Ensembl | nif-0000-33718, r3d100011196 | https://doi.org/10.17616/R3RK74, https://doi.org/10.17616/R3RK74 | SCR_008681 | EnsemblFungi | 2026-09-05 06:31:54 | 261 | ||||||||
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Ensembl Plants Resource Report Resource Website 1000+ mentions |
Ensembl Plants (RRID:SCR_008680) | data or information resource, database | Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Plants, which houses plant species. Sponsors: EnsembPlants is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute. | database, genome, plant, software, specie, taxonomic, FASEB list | has parent organization: Ensembl | Free, Freely available, | nif-0000-33715, r3d100011199 | https://doi.org/10.17616/R3CD1Q | SCR_008680 | EnsemblPlants | 2026-09-05 06:31:54 | 2191 | |||||||
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Ensembl Bacteria Resource Report Resource Website 50+ mentions |
Ensembl Bacteria (RRID:SCR_008679) | data or information resource, database | The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Bacteria, which houses bacterial species. All bacterial collections in Ensembl Bacteria have been updated with the latest data from ENA and UniProtKB. New genomes have been added to Escherichia/Shigella (3 additional genomes) and Staphylococcus (3 additional genomes). The mapping of array probes has been expanded to all genomes in the Escherichia/Shigella and Staphylococcus collections. Ensembl Bacteria also now features improved interfaces for selecting regions of circular molecules a new visualisation allowing the large scale comparison of multiple genomes. In multi-synteny view, users can select multiple genomes and observe the syntenic relationships between them. Sponsors: EnsembBacteria is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute. | escherichia, array, bacterial, bacterium, circular, database, genome, mapping, molecule, proble, shigella, software, specie, staphyococcus, taxonomic, visualization, FASEB list | has parent organization: Ensembl | r3d100011195, nif-0000-33711 | https://doi.org/10.17616/R3WD1C, https://doi.org/10.17616/R3WD1C | SCR_008679 | EnsemblBacteria | 2026-09-05 06:31:54 | 91 | ||||||||
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Isofinder: Isochore Computational Prediction Resource Report Resource Website |
Isofinder: Isochore Computational Prediction (RRID:SCR_008342) | analysis service resource, data analysis service, production service resource, service resource | Isofinder is an algorithm running on the web able to predict isochores at the sequence level. Isochores are long genome segments homogeneous in G+C. The algorithm works by moving a sliding pointer from left to right along the DNA sequence and computing the mean G+C values to the left and to the right of the pointer at each point. Additionally, the program checks whether this significance exceeds a probability threshold. If so, the sequence is cut at this point into two subsequences; otherwise, the sequence remains undivided. The procedure continues recursively for each of the two resulting subsequences created by each cut. This leads to the decomposition of a chromosome sequence into long homogeneous genome regions (LHGRs) with well-defined mean G+C contents, each significantly different from the G+C contents of the adjacent LHGRs. Most LHGRs can be identified with Bernardi''s isochores, given their correlation with biological features such as gene density, SINE and LINE (short, long interspersed repetitive elements) densities, recombination rate or single nucleotide polymorphism variability. The resulting isochore maps are available at http://bioinfo2.ugr.es/isochores/, and also at the UCSC Genome Browser (http://genome.cse.ucsc.edu/). Sponsors: Isofinder is funded by Universidad de Granada, Spain. | algorithm, chromosome, dna, genome, heterogeneous, homogeneous, isochore, segment, sequence, single nucleotide polymorphism, snp, statistic | has parent organization: University of Granada; Granada; Spain | nif-0000-25208 | SCR_008342 | Isofinder | 2026-09-05 06:31:52 | 0 | |||||||||
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Brain and Body Genetic Resource Exchange Resource Report Resource Website 1+ mentions |
Brain and Body Genetic Resource Exchange (RRID:SCR_008959) | BB-GRE | data or information resource, database | A database and associated tools for investigating the genetic basis of neurodisability. It combines phenotype information from patients with neurodevelopmental and behavioral problems with clinical genetic data, and displays this information on the human genome map. Basic access to genetic information (deletions, duplications) relating to participants with neurodevelopmental disorders is provided without an account; access to the full dataset requires an account. The genetic information that is available to view comprises potentially pathogenic copy number variation across the genome, detected by array comparative genome hybridization (aCGH) using a customized 44K oligonucleotide array. | developmental disorder, copy number, neurodevelopmental disorder, child, phenotype, genotype-phenotype, brain, genetic, gene, genotype, behavior, clinical, genome, neurodevelopment, behavioral disorder, genetic variant, development | has parent organization: King's College London; London; United Kingdom | Schizophrenia, Mental retardation, Attention deficit hyperactivity disorder, Developmental language delay, Dyslexia, Sleep disorder, Epilepsy, Dysmorphism, Neurodisability, Autism | Acknowledgement required | nlx_151987 | http://bbgre-dev.iop.kcl.ac.uk/info/about-us | SCR_008959 | BBGRE.org, Brain & Body Genetic Resource Exchange, BB-GRE database | 2026-09-05 06:31:55 | 1 | |||||
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GFINDer: Genome Function INtegrated Discoverer Resource Report Resource Website 1+ mentions |
GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) | GFINDer | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. Multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results. | annotation, statistical analysis, mining, genome, function, sequence, functional profile, gene, microarray, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Polytechnic University of Milan; Milan; Italy |
PMID:15980570 PMID:15215397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149256, biotools:gfinder | https://www.hsls.pitt.edu/obrc/index.php?page=URL1098209538, https://bio.tools/gfinder | SCR_008868 | Genome Function INtegrated Discoverer, Genome Function INtegrated Discoverer (GFINDer) | 2026-09-05 06:31:55 | 1 | |||||
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Resource for Genetic Epidemiology Research on Adult Health and Aging Resource Report Resource Website 1+ mentions |
Resource for Genetic Epidemiology Research on Adult Health and Aging (RRID:SCR_010472) | GERA | data or information resource, database | Human genetics data from an immense (78,000) and ethnically diverse population available for secondary analysis to qualified researchers through the database of Genotypes and Phenotypes (dbGaP). It offers the opportunity to identify potential genetic risks and influences on a broad range of health conditions, particularly those related to aging. The GERA cohort is part of the Research Program on Genes, Environment, and Health (RPGEH), which includes more than 430,000 adult members of the Kaiser Permanente Northern California system. Data from this larger cohort include electronic medical records, behavioral and demographic information from surveys, and saliva samples from 200,000 participants obtained with informed consent for genomic and other analyses. The RPGEH database was made possible largely through early support from the Robert Wood Johnson Foundation to accelerate such health research. The genetic information in the GERA cohort translates into more than 55 billion bits of genetic data. Using newly developed techniques, the researchers conducted genome-wide scans to rapidly identify single nucleotide polymorphisms (SNPs) in the genomes of the people in the GERA cohort. These data will form the basis of genome-wide association studies (GWAS) that can look at hundreds of thousands to millions of SNPs at the same time. The RPGEH then combined the genetic data with information derived from Kaiser Permanente''s comprehensive longitudinal electronic medical records, as well as extensive survey data on participants'' health habits and backgrounds, providing researchers with an unparalleled research resource. As information is added to the Kaiser-UCSF database, the dbGaP database will also be updated. | genotype, phenotype, genome-wide association study, saliva, dna, male, female, health condition, electronic medical record, single nucleotide polymorphism, adult human, late adult human, gene, genome |
has parent organization: NCBI database of Genotypes and Phenotypes (dbGap) has parent organization: University of California at San Francisco; California; USA |
Aging, Cardiovascular disease, Osteoarthritis, Depressive Disorder, Insomnia, Eye disease, Cancer, Diabetes | NIMH ; NIH Office of the Director ; NIA AG036607 |
Application required, Non-commercial, Data Use Certification Agreement | nlx_157735 | SCR_010472 | Genetic Epidemiology Research on Aging | 2026-09-05 06:31:56 | 9 | |||||
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Genomicus Resource Report Resource Website 50+ mentions |
Genomicus (RRID:SCR_011791) | Genomicus | data or information resource, database | A genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. | genome, gene, synteny, browser, FASEB list | is listed by: OMICtools | PMID:23193262 | OMICS_00914 | SCR_011791 | 2026-09-05 06:32:01 | 57 | ||||||||
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Plantagora Resource Report Resource Website 1+ mentions |
Plantagora (RRID:SCR_001227) | Plantagora | data or information resource, data set, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A web-based plant genome assembly simulation platform whose resources include out of the box scripts for analyzing assembly data, an on-demand web graphing tool to model your experiment, and a downloadable database with metrics and parameters from over 3,000 simulated genome assemblies. | next-generation sequencing, genome assembly, sequencing, genome, 454, illumina, simulate |
is listed by: OMICtools has parent organization: University of Arizona; Arizona; USA |
PMID:22174807 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02116 | SCR_001227 | Plantagora - a resource for plant genome assembly | 2026-09-05 06:30:36 | 1 |
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