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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Database of Interacting Proteins (DIP) Resource Report Resource Website 100+ mentions |
Database of Interacting Proteins (DIP) (RRID:SCR_003167) | DIP | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available. | blast, cellular network, ligand-receptor complex, ligand, network, protein, protein interaction, protein ligand, protein-protein interaction, protein receptor, receptor, sequence, interaction, regulatory pathway, signaling pathway, protein binding, bio.tools, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: NIH Data Sharing Repositories is related to: PSICQUIC Registry is related to: Agile Protein Interactomes DataServer has parent organization: University of California at Los Angeles; California; USA |
NIGMS | PMID:14681454 | Free, Available for download, Freely available | OMICS_01905, nif-0000-00569, r3d100010882, biotools:dip | https://dip.doe-mbi.ucla.edu/dip/Main.cgi, https://bio.tools/dip, https://doi.org/10.17616/R3431F | SCR_003167 | , Database of Interacting Proteins, DIP, Database of Interacting Proteins (DIP) | 2026-08-29 11:21:45 | 167 | ||||
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Honig Lab Resource Report Resource Website |
Honig Lab (RRID:SCR_003410) | Honig Lab | analysis service resource, data analysis service, data or information resource, data set, database, laboratory portal, organization portal, portal, production service resource, service resource, software resource | Laboratory portal, including software, web-based tools, databases and data sets, related to their research that focuses on the development and application of biophysical and bioinformatics methods aimed at understanding the structural and energetic origins of protein-protein, protein-nucleic acid, and protein-membrane interactions. Their work includes fundamental theoretical research, the development of software tools, and applications to problems of biological importance. In this regard they maintain an active collaborative computational and experimental research program on the molecular basis of cell-cell adhesion. Other problems of current interest include protein structure prediction, the organization of protein sequence/structure space, the prediction of protein function based on protein structure, the structural origins of specificity in protein-DNA interactions, RNA function and, more generally, the electrostatic properties of biological macromolecules. | electrostatic, function, adhesion, analysis, biological, biophysical, cell, dna, interaction, macromolecule, membrane, nucleic acid, protein, rna, sequence, specificity, structural, structure, protein structure, protein, protein-protein interaction, protein-nucleic acid interaction, protein-membrane interaction |
is listed by: Biositemaps has parent organization: Columbia University; New York; USA |
nif-0000-33026 | SCR_003410 | Honig Laboratory | 2026-08-29 11:21:55 | 0 | ||||||||
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DTU Center for Biological Sequence Analysis Resource Report Resource Website 1000+ mentions |
DTU Center for Biological Sequence Analysis (RRID:SCR_003590) | CBS, DTU CBS | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics. | nucleotide, sequence, amino acid, dna, microarray, molecule, immunology, protein function, protein structure, protein, post-translational, whole genome, sequence analysis |
has parent organization: Technical University of Denmark; Lyngby; Denmark is parent organization of: NESbase is parent organization of: O-GLYCBASE is parent organization of: OligoWiz is parent organization of: SignalP |
Danish National Research Foundation ; Danish Research Councils ; Danish Center for Scientific Computing ; Villum Kann Rasmussen Foundation ; Novo Nordisk Foundation ; European Union ; NIH |
nlx_12329 | http://www.cbs.dtu.dk/index.shtml | SCR_003590 | 2026-08-29 11:21:35 | 1475 | |||||||
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MODELLER Resource Report Resource Website 5000+ mentions |
MODELLER (RRID:SCR_008395) | data or information resource, portal, simulation software, software application, software resource, topical portal | Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms. | comparative, protein, structure, modelling, satisfaction, spatial, restrain, homology, 3D, alignment, sequence, hydrogen, atom, cluster |
is listed by: SoftCite has parent organization: University of California at San Francisco; California; USA |
IBM ; Intel ; NIGMS P01 GM71790; NIGMS R01 GM54762; NIGMS U54 GM62529; NIH P01 A135707; Sandler Family Supporting Foundation |
Restricted | nif-0000-30054 | SCR_008395 | 2026-08-29 11:23:14 | 5873 | ||||||||
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G protein receptor interaction feature finding instrument Resource Report Resource Website 10+ mentions |
G protein receptor interaction feature finding instrument (RRID:SCR_008343) | analysis service resource, production service resource, resource, service resource | Griffin (G-protein-receptor interacting feature finding instrument) is a high-throughput system to predict GPCR - G-protein coupling selectively with the input of GPCR sequence and ligand molecular weight. This system consists of two parts: 1) HMM section using family specific multiple alignment of GPCRs, 2) SVM section using physico-chemical feature vectors in GPCR sequence. G-protein coupled receptors (GPCR), which is composed of seven transmembrane helices, play a role as interface of signal transduction. The external stimulation for GPCR, induce the coupling with G-protein (Gi/o, Gq/11, Gs, G12/13) followed by different kinds of signal transduction to inner cell. About half of distributed drugs are intending to control this GPCR - G-protein binding system, and therefore this system is important research target for the development of effective drug. For this purpose, it is necessary to monitor, effectively and comprehensively, of the activation of G-protein by identifying ligand combined with GPCR. Since, at present, it is difficult to construct such biochemical experiment system, if the answers for experimental results can be prepared beforehand by using bioinformatics techniques, large progress is brought to G-protein related drug design. Previous works for predicting GPCR-G protein coupling selectivity are using sequence pattern search, statistical models, and HMM representations showed high sensitivity of predictions. However, there are still no works that can predict with both high sensitivity and specificity. In this work we extracted comprehensively the physico-chemical parameters of each part of ligand, GPCR and G-protein, and choose the parameters which have strong correlation with the coupling selectivity of G-protein. These parameters were put as a feature vector, used for GPCR classification based on SVM. | drug, alignment, biochemical, bioinformatic, coupling, gpcr, g-protein, helix, instrument, interface, ligand, molecular, pattern, physico-chemical, receptor interacting, sequence, signal transduction, stimulation, svm, system, technique, transmembrane, weight, instrument, equipment, hardware, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Computational Biology Research Center Core Facility |
National Institute of Advanced Industrial Science and Technology | nif-0000-25210, biotools:griffin | https://bio.tools/griffin | SCR_008343 | Griffin | 2026-08-29 11:23:13 | 21 | |||||||
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Distributed Annotation System Resource Report Resource Website 10+ mentions |
Distributed Annotation System (RRID:SCR_008427) | data or information resource, narrative resource, software resource, standard specification | The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center. | annotation, database, software, genomic, protein, sequence, visualization, data, client-server, integration, bioinformatics, genome, structure, data integration |
is listed by: 3DVC has parent organization: Uppsala University; Uppsala; Sweden |
Howard Hughes Medical Institute ; NHGRI 2-P01-HG00956 |
nif-0000-30177 | SCR_008427 | BioDAS | 2026-08-29 11:23:15 | 11 | ||||||||
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Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-08-29 11:23:30 | 3886 | |||||
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GOMO - Gene Ontology for Motifs Resource Report Resource Website 1+ mentions |
GOMO - Gene Ontology for Motifs (RRID:SCR_008864) | GOMO | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | Gene Ontology for Motifs (GOMO) is an alignment- and threshold-free comparative genomics approach for assigning functional roles to DNA regulatory motifs from DNA sequence. The algorithm detects associations between a user-specified DNA regulatory motif (expressed as a position weight matrix; PWM) and Gene Ontology terms. The original method for predicting the roles of transcription factors (TFs starts with a PWM motif describing the DNA-binding affinity of the TF. GOMO uses the PWM to score the promoter region of each gene in the genome for its likelihood to be bound by the TF. The resulting ''''affinity'''' scores are then used to test each term in the Gene Ontology for association with high-scoring genes. The algorithm was subsequently extended to leverage conserved signals using multiple, related species in a comparative approach, which greatly improves the resulting annotations. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, motif, genomics, gene ontology, function, compare, ontology or annotation editor, statistical analysis, dna binding motif, dna binding, dna, transcription factor, sequence |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Queensland; Brisbane; Australia has parent organization: MEME Suite - Motif-based sequence analysis tools |
Australian Research Council ; University of Queensland; Brisbane; Australia ; International Research Tuition Award ; NCRR R01 RR021692 |
PMID:20147307 PMID:18544606 |
Free for academic use | nlx_149250 | SCR_008864 | Gene Ontology for Motifs | 2026-08-29 11:23:14 | 3 | |||||
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PDBj - Protein Data Bank Japan Resource Report Resource Website 10+ mentions |
PDBj - Protein Data Bank Japan (RRID:SCR_008912) | PDBj | data or information resource, data repository, database, service resource, storage service resource | PDBj (Protein Data Bank Japan) maintains a centralized PDB archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU. | protein, macromolecule, structure, sequence, ligand, binding site, nmr, molecule, gold standard |
is recommended by: NIDDK Information Network (dkNET) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBe - Protein Data Bank in Europe is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Osaka University; Osaka; Japan |
Japan Science and Technology Agency ; NBDC - National Bioscience Database Center |
PDB data, Text and images are free of all copyright restrictions. You can use them free of charge. When you reprint or cite them, Please also cite us as follows: Protein Data Bank Japan (PDBj) Please also see Terms of Use page. | nlx_151484, r3d100010910 | https://doi.org/10.17616/R3RP75, https://doi.org/10.17616/R3RP75 | SCR_008912 | PDBj, Protein Data Bank Japan | 2026-08-29 11:23:28 | 46 | |||||
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BeeBase Resource Report Resource Website 50+ mentions |
BeeBase (RRID:SCR_008966) | BeeBase | analysis service resource, data analysis service, data or information resource, data set, database, production service resource, service resource | Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.BeeBase is an archive and will not be updated. The most up-to-date bee genome data is now available through the navigation bar on the HGD Home page. | genome, gene set, sequence, bee, genomics, entomology, blast, annotation, pest, pathogen, honey, beehive, insect, bee pollen, bee product, bee culture, pollination, pollinator, bio.tools, FASEB list |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: University of Missouri; Missouri; USA |
Texas Agricultural Experiment Station ; Golden Heritage Foods and Sioux Honey Association ; NHGRI 5-P41-HG000739-13; USDA 2008-35302-18804 |
PMID:21071397 | Open unspecified license, Acknowledgement requested, Data Usage Policy | nlx_152034, biotools:hgd, r3d100010925 | https://bio.tools/hgd, https://doi.org/10.17616/R3Z629 | SCR_008966 | Hymenoptera Genome Database | 2026-08-29 11:23:35 | 56 | ||||
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PRECISE Resource Report Resource Website 50+ mentions |
PRECISE (RRID:SCR_007874) | PRECISE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of interactions between amino acid residues of enzyme and its ligands. Provides summary of interactions between amino acid residues of enzyme and its various ligands including substrate and transition state analogues, cofactors, inhibitors, and products., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | enzyme, enzyme and enzyme nomenclature databases, function, align, amino acid, analogue, atom, chain, cofactor, complex, hydrogen bond, inhibitor, interaction, ligand, product, residue, sequence, structure, substrate, transition state | has parent organization: Boston University; Massachusetts; USA | NSF | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21331, SCR_008230 | http://precise.bu.edu/precisedb/ | SCR_007874 | Predicted and Consensus Interaction Sites in Enzymes | 2026-08-29 11:23:19 | 53 | |||||
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GoatMap Database Resource Report Resource Website |
GoatMap Database (RRID:SCR_008144) | data or information resource, data repository, database, portal, service resource, storage service resource, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This website contains information about the mapping of the caprine genome. It contains loci list, phenes list, cartography, gene list, and other sequence information about goats. This website contains 731 loci, 271 genes, and 1909 homologue loci on 112 species. It also allows users to summit their own data for Goatmap. ARK-Genomics is not-for-profit and has collaborators from all over the world with an interest in farm animal genomics and genetics. ARK-Genomics was initially set up in 2000 with a grant awarded from the BBSRC IGF (Investigating Gene Function) initiative and from core resources of the Roslin Institute to provide a laboratory for automated analysis of gene expression using state-of-the-art genomic facilities. Since then, ARK-Genomics has expanded considerably, building up considerable expertise and resources. | farm, gene, animal, caprine, cartography, genome, genomic, goat, homologue, locus, map, mapping, phene, sequence | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20978 | SCR_008144 | GoatMap | 2026-08-29 11:23:00 | 0 | |||||||||
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Bacterial Genomes Resource Report Resource Website 10+ mentions |
Bacterial Genomes (RRID:SCR_008141) | data analysis software, data or information resource, data processing software, database, software application, software resource | This website includes a list of projects that the Sanger Institute is currently working on or completed. All projects consist of the genomic sequencing of different bacteria. Each description of the bacteria includes its classification, a description, and the types of diseases that the bacteria is likely to cause. The Sanger Institute bacterial sequencing effort is concentrated on pathogens and model organisms. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing users to search the sequences with their own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing you to search the sequences with your own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. The primary sequence viewer and annotation tool, Artemis is available for download. This is a portable Java program which is used extensively within the Microbial Genomes group for the analysis and annotation of sequence data from cosmids to whole genomes. The Artemis Comparison Tool (ACT) is also useful for interactive viewing of the comparisons between large and small sequences. | bacteria, bacterial, classification, description, disease, genomic, model, organism, pathogen, sequence, sequencing, model |
is listed by: 3DVC has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
nif-0000-20963 | SCR_008141 | Bacterial Genomes | 2026-08-29 11:23:08 | 12 | |||||||||
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Human Gut Microbiome Initiative Resource Report Resource Website |
Human Gut Microbiome Initiative (RRID:SCR_008137) | data or information resource, database, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2022. Human Gut Microbiome Initiative (HGMI) seeks to provide simply annotated, deep draft genome sequences for 100 cultured representatives of the phylogenetic diversity documented by 16S rRNA surveys of the human gut microbiota. Humans are supra-organisms, composed of 10 times more microbial cells than human cells. Therefore, it seems appropriate to consider ourselves as a composite of many species - human, bacterial, and archaeal - and our genome as an amalgamation of human genes and the genes in ''our'' microbial genomes (''microbiome''). In the same sense, our metabolome can be considered to be a synthesis of co-evolved human and microbial traits. The total number of genes present in the human microbiome likely exceeds the number of our H. sapiens genes by orders of magnitude. Thus, without an understanding of our microbiota and microbiome, it not possible to obtain a complete picture of our genetic diversity and of our normal physiology. Our intestine is home to our largest collections of microbes: bacterial densities in the colon (up to 1 trillion cells/ml of luminal contents) are the highest recorded for any known ecosystem. The vast majority of phylogenetic types in the distal gut microbiota belong to just two divisions (phyla) of the domain Bacteria - the Bacteroidetes and the Firmicutes. Members of eight other divisions have also been identified using culture-independent 16S rRNA gene-based surveys. Metagenomic studies of complex microbial communities residing in our various body habitats are limited by the availability of suitable reference genomes for confident assignment of short sequence reads generated by highly parallel DNA sequencers, and by knowledge of the professions (niches) of community members. Therefore, HGMI, which represents a collaboration between Washington University''s Genome Center and its Center for Genome Sciences, seeks to provide simply annotated, deep draft genome sequences for 100 cultured representatives of the phylogenetic diversity documented by 16S rRNA surveys of the human gut microbiota. | ecosystem, firmicutes, bacterial, bacteroidetes, body, cell, diversity, genome, gut, habitat, human, metabolom, microbial, microbiome, microbiota, phylogenetic, rrna, sequence, specie, synthesis | has parent organization: Washington University in St. Louis; Missouri; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20960 | http://genome.wustl.edu/projects/athaliana/ | SCR_008137 | HGMI | 2026-08-29 11:23:08 | 0 | |||||||
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dbEST Resource Report Resource Website 100+ mentions |
dbEST (RRID:SCR_008132) | data or information resource, data repository, database, service resource, storage service resource | Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms. | data, sequence, single, pass, cDNA, express, tag, bio.tools, gold standard |
is listed by: Debian is listed by: bio.tools has parent organization: NCBI |
PMID:8401577 | biotools:dbest, nif-0000-20937, r3d100010648 | http://www.ncbi.nlm.nih.gov/dbEST/, https://bio.tools/dbest, https://doi.org/10.17616/R3FG8P | SCR_008132 | database Expressed Sequence Tag (EST), database Expressed Sequence Tag | 2026-08-29 11:23:26 | 186 | |||||||
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Gene Regulation Databases Resource Report Resource Website 100+ mentions |
Gene Regulation Databases (RRID:SCR_008033) | Gene Regulation Public Databases | data or information resource, portal, topical portal | In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers academic and non-profit organizations free access to reduced functionality versions of their products. TRANSFAC Professional provides gene regulation analysis solutions, offering the most comprehensive collection of eukaryotic gene regulation data. The professional paid subscription gives customers access to up-to-date data and tools not available in the free version. The public databases currently available for academic and non-profit organizations are: * TRANSFAC: contains data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. * TRANSPATH: provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signaling components.TRANSPATH focuses on signaling cascades that change the activities of transcription factors and thus alter the gene expression profile of a given cell. * PathoDB: is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. * S/MARt DB: presents data on scaffold or matrix attached regions (S/MARs) of eukaryotic genomes, as well as about the proteins that bind to them. S/MARs organize the chromatin in the form of functionally independent loop domains gained increasing support. Scaffold or Matrix Attached Regions (S/MARs) are genomic DNA sequences through which the chromatin is tightly attached to the proteinaceous scaffold of the nucleus. * TRANSCompel: is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signaling pathways. * PathoSign Public: is a database which collects information about defective cell signaling molecules causing human diseases. While constituting a useful data repository in itself, PathoSign is also aimed at being a foundational part of a platform for modeling human disease processes. | element, eukaryote, eukaryotic, expression, functionally, gene, genome, alignment, bind, binding site, cell, chromatin, collaborative, component, coupling, disease, dna, domain, human, matrix, molecular weight, molecule, mononucleotide, network, nucleotide, nucleus, pathological, protein, region, regulated, regulatory, scientific research, sequence, signaling, signal pathway, transcription factor, molecular neuroanatomy resource |
lists: TRANSFAC has parent organization: BIOBASE Corporation |
BIOBASE | nif-0000-10230 | SCR_008033 | gene-regulation.com: Public Databases for Academic and Non-profit Organizations | 2026-08-29 11:23:23 | 130 | |||||||
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HPV Sequence Database Resource Report Resource Website 1+ mentions |
HPV Sequence Database (RRID:SCR_008154) | data or information resource, database, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 23, 2016. The Human Papillomaviruses Database collects, curates, analyzes, and publishes genetic sequences of papillomaviruses and related cellular proteins. It includes molecular biologists, sequence analysts, computer technicians, post-docs and graduate research assistants. This Web site has two main branches. The first contains our four annual data books of papillomavirus information, called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. and the second contains papillomavirus genetic sequence data. There is also a New Items location where we store the latest changes to the database or any other current news of interest. Besides the compendium, we also provide genetic sequence information for papilloma viruses and related cellular proteins. Each year they publish a compendium of papillomavirus information called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. which can now be downloaded from this Web site. | gene, genetic, alignment, amino acid, biologist, cellular protein, genome, human, molecular, papilloma, papillomavirus, phylogenetic, sequence, virus | has parent organization: Los Alamos National Laboratory | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21000 | http://www.stdgen.lanl.gov/ | SCR_008154 | HPVSD | 2026-08-29 11:23:27 | 4 | |||||||
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Genomatix Software: Understanding Gene Regulation Resource Report Resource Website 500+ mentions |
Genomatix Software: Understanding Gene Regulation (RRID:SCR_008036) | data analysis software, data or information resource, data processing software, database, narrative resource, portal, short course material, software application, software resource, topical portal, training material | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 13,2026. Genomatix is a privately held company that offers software, databases, and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology. Its multilayer integrative approach is a working implementation of systems biology principles. Genomatix combines sequence analysis, functional promoter analysis, proprietary genome annotation, promoter sequence databases, comparative genomics, scientific literature data mining, pathway databases, biological network databases, pathway analysis, network analysis, and expression profiling into working solutions and pipelines. It also enables better understanding of biological mechanisms under different conditions and stimuli in the biological context of your data. Some of Genomatix'' most valuable assets are the strong scientific background and the years of experience in research & discovery as well as in development & application of scientific software. Their firsthand knowledge of all the complexities involved in the in-silico analysis of biological data makes them a first-rate partner for all scientific projects involving the evaluation of gene regulatory mechanisms. The Genomatix team has more than a decade of scientific expertise in the successful application of computer aided analysis of gene regulatory networks, which is reflected by more than 150 peer reviewed scientific publications from Genomatix'' scientists More than 35,000 researchers in industry and academia around the world use this technology. The software available in Genomatix are: - GenomatixSuite: GenomatixSuite is our comprehensive software bundle including ElDorado, Gene2Promoter, GEMS Launcher, MatInspector and MatBase. GenomatixSuite PE also includes BiblioSphere Pathway Edition. Chromatin IP Software - RegionMiner: Fast, extensive analysis of genomic regions. - ChipInspector: Discover the real power of your microarray data. Genome Annotation Software - ElDorado: Extended Genome Annotation. - Gene2Promoter: Retrieve & analyze promoters - GPD: The Genomatix Promoter Database, which is now included with Gene2Promoter. Knowledge Mining Software - BiblioSpere : The next level of pathway/genomics analysis. - LitInspector: Literature and pathway analysis for free. Sequence Analysis Software - GEMS Launcher: Our integrated collection of sequence analysis tools. - MalInspector: Search transcription factor binding sites - MatBase: The transcription factor knowledge base. Other (no registration required) Software - DiAlign: Multiple alignment of DNA/protein sequence. - Genomatix tools: Various small tools for sequence statistics, extraction, formatting, etc. | effect, expression, functional, gene, genome, alignment, analysis, annotation, biological, cascade, cell, data, dna, in-silico analysis, mechanism, metabolic pathway, microarray, mining, molecular, network, pathway, promoter, protein, region, regulation, scientific, sequence, signaling, software, stimulus, systems biology, technology, text mining, transcription, FASEB list | has parent organization: Genomatix Solutions | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10236 | http://www.genomatix.de/products/index.html | SCR_008036 | Genomatix | 2026-08-29 11:23:06 | 887 | |||||||
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RIKEN Omics Science Center Resource Report Resource Website |
RIKEN Omics Science Center (RRID:SCR_008241) | data or information resource, disease-related portal, portal, research forum portal, topical portal | Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level. | expression, gene, genome, human, intracellular, life, living, model organisms and comparative genomics databases, molecule, omics, organism, pathway, protein, proteome, science, sequence, technology, transcriptome | is parent organization of: FANTOM DB | RIKEN Yokohama Institute Yokohama Research Promotion Division of Japan | nif-0000-21361 | SCR_008241 | RIKEN OSC | 2026-08-29 11:23:28 | 0 | ||||||||
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Dictyostelium discoideum genome database Resource Report Resource Website 100+ mentions |
Dictyostelium discoideum genome database (RRID:SCR_006643) | dictyBase, dictyBase gene name, dictyBase REF, DictyBase | biomaterial supply resource, material resource, organism supplier | Model organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ''''reference genome'''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries. | genome, sequence, est, literature, gene model, functional annotation, reference genome, gene, antibody, cdna, bacteria, dictyostelium discoideum, dictyostelium purpureum, dictyostelium fasciculatum, polysphondylium pallidium, bio.tools |
is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Textpresso has parent organization: Northwestern University; Illinois; USA has parent organization: Baylor University; Texas; USA has parent organization: University of Cologne; Cologne; Germany is parent organization of: Dictyostelium Discoideum Anatomy Ontology is parent organization of: Dictyostelium Anatomy Ontology is parent organization of: dictyBase - Teaching Tools Using Dictyostelium discoideum |
European Union ; NHGRI HG0022; NIGMS GM087371; NIGMS GM64426 |
PMID:23172289 PMID:21087999 PMID:18974179 PMID:14681427 PMID:16381903 |
biotools:dictybase, nif-0000-20974, SCR_008149, nif-0000-02751, OMICS_03158 | https://bio.tools/dictybase | http://genome.imb-jena.de/dictyostelium/ | SCR_006643 | dictyBase gene name, dictyBase REF, Dicty, dictyBase, Dictyostelium discoideum | 2026-08-29 11:22:46 | 315 |
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