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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GeneSeer Resource Report Resource Website |
GeneSeer (RRID:SCR_002626) | GeneSeer | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database to access gene information through common names and allows identification of homologs and paralogs for a given gene. This publicly available tool leverages public sequence data, gene metadata information, and other publicly available data to calculate and display orthologous and paralogous gene relationships for all genes from several species, including yeasts, insects, worms, vertebrates, mammals, and primates such as humans. | gene, homolog, paralog, genome, search engine, ortholog | PMID:16176584 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156048 | http://katahdin.mssm.edu/geneseer/scripts/main.pl | http://geneseer.cshl.org/ | SCR_002626 | 2026-09-19 12:56:36 | 0 | ||||||
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MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation Resource Report Resource Website 10+ mentions |
MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation (RRID:SCR_003077) | MAPPER, MAPPER 2, | data or information resource, database, service resource | A platform composed of three modules: the Database, the Search Engine, and rSNPs, for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC and JASPAR data with the search power of profile hidden Markov models (HMMs). The Database contains putative TFBSs found in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each gene, they scanned the region from 10,000 base pairs upstream of the transcript start to 50 base pairs downstream of the coding sequence start against all their models. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs. The Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs. | transcription factor binding site, gene promoter, intron, non-coding exon, transcription factor, chromosome, gene, homolog, rsnp, single nucleotide polymorphism, search engine |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA is parent organization of: rSNPs MAPPER |
PMID:15608292 PMID:15799782 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01877, nif-0000-03101 | http://bio.chip.org/mapper | SCR_003077 | Multi-genome Analysis of Positions and Patterns of Elements of Regulation, MAPPER 2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation, MAPPER database | 2026-09-19 12:56:38 | 11 | |||||
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Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome Resource Report Resource Website |
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) | HEFalMp | data or information resource, database, service resource | HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool. | human, map, gene, functional, pathway, disease, genomic, analysis, microarray, dna, protein, sequence | has parent organization: Princeton University; New Jersey; USA | New Jersey Commission on Cancer Research ; PhRMA Foundation 2007RSGl9572; NIGMS R01 GM071966; NSF DBI-0546275; NSF IIS-0513552; NHGRI T32 HG003284; NIGMS P50 GM071508 |
PMID:19246570 | nif-0000-37186 | SCR_003506 | Human Experimental / FunctionAL MaPper, Human Experimental/FunctionAL MaPper | 2026-09-19 12:56:40 | 0 | ||||||
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GeneFisher Resource Report Resource Website 10+ mentions |
GeneFisher (RRID:SCR_003060) | GeneFisher, GeneFisher2 | analysis service resource, data analysis service, production service resource, service resource | A web-based program for designing degenerate primers. The procedure leads to isolation of genes in a target organism using multiple alignments of related genes from different organisms. The term gene fishing refers to the technique where PCR is used to isolate a postulated but unknown target sequence from a pool of DNA. | primer design, gene, degenerate primer, degenerate, primer, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:8877506 | Free, Freely available | biotools:genefisher, OMICS_02341 | https://bio.tools/genefisher | SCR_003060 | GeneFisher2 - Interactive PCR Primer Design | 2026-09-19 12:56:38 | 39 | |||||
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SynSysNet Resource Report Resource Website 1+ mentions |
SynSysNet (RRID:SCR_003180) | SynSysNet | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A curated database for synaptic proteins that provides adequate definitions of pre- and post-synaptic proteins, proteins present in sub-domains of the synapse, e.g. the synaptic vesicle and associated proteins, lipid rafts and postsynaptic density. In addition to data that was and will be gathered from the experiments conducted within SynSys - A European expertise Network on building the synapse, they have extracted and manually curated all relevant data on these proteins from other sources and provided an ontology for these. Novel splice forms are being identified that can be matched with proteomics data. Information on proteins, their 3D structure, binding small molecules Protein-Protein-Interactions (PPIs) and Compound-Protein-Interactions are integrated. Proteins or compounds can be searched and Interactive Networks can be visualized. The point Diseases present neurological diseases, to illustrate the role of SynSysNet in the medication. | gene, synapse, protein, interaction, compound, disease, structure, model, compound, protein-drug interaction, protein-protein interaction, pathway, drug-target, small molecule, interaction network, homology, drug, drug-target interaction, compound-protein interaction, visualization, proteomics, network |
is listed by: OMICtools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: KEGG has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
Huntington's disease, Chorea Huntington, Epilepsy, Multiple Sclerosis, Parkinson's disease, Schizophrenia, Neurological disease | European Union Seventh FPSYNSYS 242167; DFG GRK1772; DFG GRK1360 |
PMID:23143269 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156893, OMICS_01914 | SCR_003180 | SynSysNet - Synaptic Proteins Database | 2026-09-19 12:56:39 | 3 | ||||
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LIPID MAPS Proteome Database Resource Report Resource Website 1+ mentions |
LIPID MAPS Proteome Database (RRID:SCR_003062) | LMPD | data or information resource, database | Database of lipid related proteins representing human and mouse proteins involved in lipid metabolism. Collection of lipid related genes and proteins contains data for genes and proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio. | gene, protein, lipid, metabolism, metabolomics |
uses: Gene Ontology uses: KEGG uses: UniProt uses: Entrez Gene uses: ENZYME has parent organization: LIPID Metabolites And Pathways Strategy |
NIGMS | PMID:16381922 | Free, Freely available | nif-0000-03085 | http://www.lipidmaps.org/data/proteome/index.cgi | SCR_003062 | LIPID MAPS Proteome Database (LMPD) | 2026-09-19 12:56:38 | 3 | ||||
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IPD - Immuno Polymorphism Database Resource Report Resource Website 10+ mentions |
IPD - Immuno Polymorphism Database (RRID:SCR_003004) | IPD | data or information resource, database | A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines. | polymorphic gene, immune system, gene, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
European Union contract QLRI-CT-200!-01325; NCI P01 111412 |
PMID:19875415 PMID:18449992 PMID:15608253 |
biotools:ipd, nif-0000-03038, r3d100010797 | https://bio.tools/ipd, https://doi.org/10.17616/R3KK7K | SCR_003004 | IPD-The Immuno Polymorphism Database, IPD - The Immuno Polymorphism Database | 2026-09-19 12:56:38 | 26 | |||||
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Coddle-Codons Optimized to Discover Deleterious LEsions Resource Report Resource Website 10+ mentions |
Coddle-Codons Optimized to Discover Deleterious LEsions (RRID:SCR_003003) | CODDLE | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Web-accessible program that identifies the region(s) of a user-selected gene and of its coding sequence (CDS) where the anticipated point mutations are most likely to result in deleterious effects on the gene's function. CODDLe separately handles 1) the prediction of changes which should truncate the protein and destabilize the RNA - nonsense changes and splice junction changes, and 2) the prediction of missense changes which should alter function of the gene product - those in conserved amino acid blocks in the CDS. Because the region(s) identified will be PCR amplified by the user and that amplicon will be used for polymorphism discovery, the application delivers primer pairs selected by Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998)Primer3.) After selecting a primer pair, CODDLe returns a window with the selected amplicon and tabulates the effects of all possible polymorphisms which could be detected in that amplicon. CODDLe will not identify the regions of a gene where polymorphisms are most likely to be discovered. Others have shown that naturally occurring SNPs are found more often in the untranslated regions of a gene. | codon, deleterious lesion, gene, coding, sequence, mutation, primer, protein sequence, cdna, sequence alignment, coding sequence |
is listed by: 3DVC has parent organization: Fred Hutchinson Cancer Center |
DOE ; Office of Energy Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30262 | SCR_003003 | Choosing codons to Optimize Discovery of Deleterious Lesions, Codons Optimized to Discover Deleterious LEsions | 2026-09-19 12:56:38 | 16 | ||||||
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Mammalian Mitochondrial Genomics Database Resource Report Resource Website |
Mammalian Mitochondrial Genomics Database (RRID:SCR_003084) | MamMiBase | data or information resource, database | Database developed to assist the phylogeneticist user in retrieving individual gene sequence alignments for genes in complete mammalian mitochondrial genomes. Data retrieval in MamMiBase requires three stages. At the first stage, the user must select the mammalian species or group that (s)he wishes to study. In the second stage, the user will select the outgroup from a list that included all species selected in the first stage plus Xenopus laevis and Gallus gallus. Finally, at the third stage, the user will select individual mitochondrial gene alignments or a phylogenetic tree that (s)he wishes to download. | phylogeny, mitochondrial, genome, gene, sequence | has parent organization: National Laboratory for Scientific Computing; Rio de Janeiro; Brazil | Brazilian Ministry of Science Technology and Innovation ; National Research Council ; Rio de Janeiro Science Foundation ; FAPERJ |
PMID:15713730 | Free, Freely available | nif-0000-03099 | SCR_003084 | 2026-09-19 12:56:38 | 0 | ||||||
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Type-III-Secretion-System related database Resource Report Resource Website |
Type-III-Secretion-System related database (RRID:SCR_002941) | T3DB | data or information resource, database | Database aimed to annotate all bacterial Type III Secretion System (T3SS) related structure, effector, regulator, and auxiliary genes. | type iii secretion system, gene, protein, ortholog |
is listed by: OMICtools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:22545727 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05160 | SCR_002941 | T3SS-related Database | 2026-09-19 12:56:37 | 0 | ||||||
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PPDB: Plant Promoter Database Resource Report Resource Website |
PPDB: Plant Promoter Database (RRID:SCR_003395) | PPDB | data or information resource, database | A plant promoter database that provides information on transcription start sites (TSSs), core promoter structure and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles. | gene, transcription start site, promoter structure, promoter, regulatory element group, homolog |
is listed by: OMICtools has parent organization: Gifu University; Gifu; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:24194597 PMID:17947329 |
Free, Available for download, Freely available | nif-0000-03329, OMICS_01874 | http://ppdb.gene.nagoya-u.ac.jp/cgi-bin/index.cgi | SCR_003395 | Plant Promoter Database | 2026-09-19 12:56:39 | 0 | ||||
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Integrated Molecular Interaction Database Resource Report Resource Website 1+ mentions |
Integrated Molecular Interaction Database (RRID:SCR_003546) | IMID | data or information resource, database | Database for molecular interaction information integrated with various other bio-entity information, including pathways, diseases, gene ontology (GO) terms, species and molecular types. The information is obtained from several manually curated databases and automatic extraction from literature. There are protein-protein interaction, gene/protein regulation and protein-small molecule interaction information stored in the database. The interaction information is linked with relevant GO terms, pathway, disease and species names. Interactions are also linked to the PubMed IDs of the corresponding abstracts the interactions were obtained from. Manually curated molecular interaction information was obtained from BioGRID, IntAct, NCBI Gene, and STITCH database. Pathway related information was obtained from KEGG database, Pathway Interaction database and Reactome. Disease information was obtained from PharmGKB and KEGG database. Gene ontology terms and related information was obtained from Gene Ontology database and GOA database. | pathway, disease, gene ontology, specie, interaction, molecular, protein-protein interaction, gene/protein regulation, protein-small molecule interaction, gene, protein, regulation |
is related to: Gene Ontology is related to: Entrez Gene is related to: Pathway Commons is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Search Tool for Interactions of Chemicals is related to: KEGG is related to: Pathway Interaction Database is related to: Reactome is related to: PharmGKB has parent organization: Florida State University; Florida; USA |
PMID:22238258 | nlx_157667 | SCR_003546 | 2026-09-19 12:56:40 | 1 | ||||||||
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Cotton EST Database Resource Report Resource Website 10+ mentions |
Cotton EST Database (RRID:SCR_003301) | Cotton EST Database | data or information resource, database | Database platform for cotton expressed sequence tag (EST)-related information, covering assembled contigs, function annotation, analysis of GO and KEGG, SNP, miRNA, SSR-related marker information. | expressed sequence tag, contig, indel mutant, single nucleotide polymorphism, transcription factor, protein kinase, gene, mirna, blast, est-simple sequence repeat, simple sequence repeat, pathway, function |
is related to: Gene Ontology is related to: KEGG has parent organization: East Carolina University; Carolina; USA |
PMID:22087239 | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100011232 | https://doi.org/10.17616/R3X63C | http://www.leonxie.com/ | SCR_003301 | 2026-09-19 12:56:39 | 10 | |||||
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Babelomics Resource Report Resource Website 100+ mentions |
Babelomics (RRID:SCR_002969) | Babelomics | analysis service resource, data analysis service, production service resource, service resource | An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool | platform, analysis, transcriptomics, proteomics, genomics, normalization, clustering, gene, mirna, protein, interaction, text mining, genotyping, bioentity, functional profiling, statistical analysis, functional annotation, regulatory motif, microarray, fatigo, biclustering, networkminer, gepas, gene expression, FASEB list |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG is related to: TRANSFAC is related to: JASPAR has parent organization: CIPF Bioinformatics and Genomics Department |
Spanish Ministry of Science and Innovation BIO2008-04212; Spanish Ministry of Science and Innovation CEN-2008-1002; Red Temtica de Investigacion Cooperativa en Cancer RD06/0020/1019; Instituto de Salud Carlos III |
PMID:20478823 PMID:18515841 PMID:16845052 PMID:14990455 PMID:15980512 PMID:17478504 |
Free for academic use, Account required | OMICS_00748, nif-0000-30144 | http://www.fatigo.org/, http://www.gepas.org/, http://babelomics3.bioinfo.cipf.es | http://www.babelomics.org | SCR_002969 | Babelomics 4: Gene Expression and Functional Profiling Analysis Suite, Babelomics 4 | 2026-09-19 12:56:38 | 138 | |||
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ResponseNet Resource Report Resource Website 1+ mentions |
ResponseNet (RRID:SCR_003176) | ResponseNet | analysis service resource, data analysis service, production service resource, service resource | WebServer that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins and genes, such as a set of disease-associated proteins and a set of differentially expressed disease genes, and a molecular interaction network (i.e., interactome). The output is a sparse, high-probability interactome sub-network connecting the two sets that is biased toward signaling pathways. This sub-network exposes additional proteins that are potentially involved in the studied condition and their likely modes of action. Computationally, it is formulated as a minimum-cost flow optimization problem that is solved using linear programming. | interactome, gene, protein, signaling pathway, signaling, regulatory, pathway, regulatory pathway, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel |
PMID:23761447 PMID:21576238 |
Free, Freely available | biotools:responsenet, OMICS_01562 | https://bio.tools/responsenet | http://netbio.bgu.ac.il/respnet/ | SCR_003176 | 2026-09-19 12:56:39 | 4 | |||||
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Gene Reference into Function Resource Report Resource Website 10+ mentions |
Gene Reference into Function (RRID:SCR_003436) | GeneRIF | data or information resource, database | A database and annotation tool that provides a simple mechanism to allow scientists to add to the functional annotation of genes described in Gene. To be processed, a valid Gene ID must exist for the specific gene, or the Gene staff must have assigned an overall Gene ID to the species. The latter case is implemented via records in Gene with the symbol NEWENTRY. | functional annotation, gene, function |
is related to: Entrez Gene has parent organization: NCBI |
NIH | PMID:17094227 PMID:23725347 |
Free, Freely available | nlx_157765 | SCR_003436 | GeneRIF: Gene Reference into Function | 2026-09-19 12:56:40 | 14 | |||||
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GeneReviews Resource Report Resource Website 100+ mentions |
GeneReviews (RRID:SCR_006560) | GeneReviews | data or information resource, database | Provides clinically relevant and medically actionable information for inherited conditions in standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families. Searchable book of expert-authored, peer-reviewed disease descriptions presented in standardized format and focused on clinically relevant and medically actionable information on diagnosis, management, and genetic counseling of patients and families with specific inherited conditions. | genetics, disease, clinical, diagnosis, management, genetic counseling, gene, chromosomal locus, phenotype, allele, locus, mutation |
is used by: NIF Data Federation is listed by: OMICtools has parent organization: NCBI has parent organization: University of Washington; Seattle; USA |
Inherited disease | PMID:20301295 | Acknowledgement required, Protected by copyright | OMICS_00269 | SCR_006560 | 2026-09-19 12:56:58 | 127 | ||||||
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DECIPHER Resource Report Resource Website 1000+ mentions |
DECIPHER (RRID:SCR_006552) | DECIPHER | data or information resource, database | Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes. | chromosomal imbalance, phenotype, chromosome, gene, genome, deletion, duplication, copy number, genotype, polymorphism, FASEB list |
is used by: MARRVEL is listed by: OMICtools is related to: Deciphering Developmental Disorders is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Microdeletion Syndrome, Overgrowth syndrome, Microduplication syndrome, Deletion syndrome, Duplication syndrome, Wolf-Hirschhorn Syndrome, Williams-Beuren Syndrome, Smith-Magenis Syndrome, Etc | Wellcome Trust WT077008 | PMID:19344873 | Acknowledgement required | nlx_151653, OMICS_00265 | SCR_006552 | Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, Database of Chromosomal Imbalance Phenotype in Humans using Ensembl Resources, Decipher | 2026-09-19 12:56:58 | 1991 | ||||
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BioGPS: The Gene Portal Hub Resource Report Resource Website 500+ mentions |
BioGPS: The Gene Portal Hub (RRID:SCR_006433) | BioGPS | data or information resource, database | An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database. | gene, ortholog, plug-in, report, literature, genetics, expression, reagent, protein, pathway, snp, genomics, gene annotation, function, FASEB list |
is listed by: Biositemaps is related to: bioDBcore is related to: aGEM has parent organization: Scripps Research Institute |
Novartis Research Foundation ; NIGMS R01GM083924 |
PMID:19919682 | Free, The community can contribute to this resource | r3d100012402, nif-0000-10168 | http://biogps.gnf.org/, https://doi.org/10.17616/R33J20 | SCR_006433 | 2026-09-19 12:56:58 | 814 | |||||
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BacMap: Bacterial Genome Atlas Resource Report Resource Website 1+ mentions |
BacMap: Bacterial Genome Atlas (RRID:SCR_006988) | BacMap | atlas, data or information resource, database | An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes. It uses a visualization tool (CGView) to generate high-resolution circular genome maps from sequence feature information. Each map includes an interface that allows the image to be expanded and rotated. In the default view, identified genes are drawn to scale and colored according to coding directions. When a region of interest is expanded, gene labels are displayed. Each label is hyperlinked to a custom ''gene card'' which provides several fields of information concerning the corresponding DNA and protein sequences. Each genome map is searchable via a local BLAST search and a gene name/synonym search. A complete listing of the species and strains in the BacMap database is available on the BacMap homepage. Below each species/strain name is a list of the sequenced chromosomes and plasmids that are available. Some features of BacMap include: * Maps are available for 2023 bacterial chromosomes. * Each map supports zooming and rotation. * Map gene labels are hyperlinked to detailed textual annotations. * Maps can be explored manually, or with the help of BacMap''s built in text search and BLAST search. * A written synopsis of each bacterial species is provided. * Several charts illustrating the proteomic and genomic characteristics of each chromosome are available. * Flat file versions of the BacMap gene annotations, gene sequences and protein sequences can be downloaded. BacMap can be used to: * Obtain basic genome statistics. * Visualize the genomic context of genes. * Search for orthologues and paralogues in a genome of interest. * Search for conserved operon structure. * Look for gene content differences between bacterial species. * Obtain pre-calculated annotations for bacterial genes of interest. | gene, gene annotation, gene sequence, genome, bacteria, chromosome, protein sequence | has parent organization: University of Alberta; Alberta; Canada | Alberta Science Research Authority ; Western Economic Diversification ; Genome Canada ; Genome Prairie ; Western Economic Diversification Canada |
PMID:15608206 | Free, Acknowledgement requested | nif-0000-02591, r3d100012724 | https://doi.org/10.17616/R35502 | SCR_006988 | BacMap: An Interactive Atlas for Exploring Bacterial Genomes, BacMap genome atlas | 2026-09-19 12:57:01 | 5 |
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