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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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bioRxiv Resource Report Resource Website 1000+ mentions |
bioRxiv (RRID:SCR_003933) | bioRxiv | data or information resource, portal, community building portal, database | A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version. | preprint, life science, bio.tools, FASEB list |
is used by: PrePubMed is listed by: LabWorm is listed by: bio.tools is listed by: Debian is related to: Overleaf has parent organization: Cold Spring Harbor Laboratory |
Free, Acknowledgement requested, The community can contribute to this resource | nlx_158302, biotools:bioRxiv | https://bio.tools/bioRxiv | SCR_003933 | bioRxiv - the preprint server for biology | 2026-02-17 10:00:08 | 1246 | ||||||
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Git Resource Report Resource Website 50+ mentions |
Git (RRID:SCR_003932) | software development tool, version source control system, software application, software resource | A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows. | version control, distributed, bio.tools |
is used by: DataLad is used by: G-Node Data Infrastructure Services is listed by: bio.tools is listed by: Debian works with: git-annex |
GNU General Public License, v2 | nlx_158301, biotools:Git | https://bio.tools/Git | SCR_003932 | 2026-02-17 10:00:31 | 66 | ||||||||
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PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | storage service resource, data or information resource, database, service resource, data repository | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors 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: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem https://doi.org/10.17616/R3GW37 |
SCR_004284 | 2026-02-17 10:00:27 | 13540 | ||||||
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PDBe - Protein Data Bank in Europe Resource Report Resource Website 50+ mentions |
PDBe - Protein Data Bank in Europe (RRID:SCR_004312) | PDBe | storage service resource, data or information resource, database, service resource, data repository | The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules. | x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standard, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: EMDataResource.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute is parent organization of: Electron Microscopy Data Bank at PDBe (MSD-EBI) works with: MOLEonline |
European Molecular Biology Laboratory; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; MRC ; CCP4 |
PMID:21045060 PMID:21460450 PMID:19858099 |
r3d100012791, biotools:pdbe, nlx_32372 | https://bio.tools/pdbe https://doi.org/10.17616/R3J226 |
SCR_004312 | Protein DataBank Europe, Protein DataBank in Europe, PDBe, Protein Data Bank in Europe, Protein Data Bank Europe, Macromolecular Structure Database | 2026-02-17 10:00:39 | 52 | |||||
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Stem Cell Discovery Engine Resource Report Resource Website 50+ mentions |
Stem Cell Discovery Engine (RRID:SCR_004453) | SCDE | storage service resource, data or information resource, production service resource, analysis service resource, database, service resource, software resource, source code, data repository | An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket. | stem cell, analysis, cancer stem cell, galaxy, gene, pathway, molecular signature, tissue, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard T.H. Chan School of Public Health |
Cancer | NCI 1RC2CA148222-01 | PMID:22121217 | Free, The community can contribute to this resource | biotools:scde_discovery, nlx_44656 | https://bio.tools/scde_discovery | SCR_004453 | Harvard Stem Cell Discovery Engine, SCDE - Stem Cell Discovery Engine | 2026-02-17 10:00:16 | 57 | |||
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Tree and reticulogram REConstruction Resource Report Resource Website 10+ mentions |
Tree and reticulogram REConstruction (RRID:SCR_004497) | T-REX | production service resource, analysis service resource, service resource, software resource, data analysis service | A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. | phylogenetic tree, analysis, visualization, network, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Quebec in Montreal; Quebec; Canada |
PMID:22675075 | biotools:t-rex, OMICS_04264 | https://bio.tools/t-rex | SCR_004497 | Trex-online | 2026-02-17 10:00:17 | 32 | ||||||
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DER Finder Resource Report Resource Website 1+ mentions |
DER Finder (RRID:SCR_004250) | DER Finder | software application, data processing software, software resource, software toolkit, software library | R package for differential expression analysis of RNA-seq data. | differential expression, rna-seq, false discovery rate, genomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24398039 | Free, Public | biotools:derfinder, OMICS_02208 | https://bio.tools/derfinder | SCR_004250 | derfinder | 2026-02-17 10:00:12 | 5 | |||||
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Transporter Classification Database Resource Report Resource Website 100+ mentions |
Transporter Classification Database (RRID:SCR_004490) | TCDB, TC | software application, storage service resource, data or information resource, production service resource, data processing software, data analysis software, analysis service resource, database, service resource, software resource, source code, data analysis service, data repository | Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run. | membrane transport, protein sequence, transporter, bio.tools, FASEB list |
is recommended by: National Library of Medicine is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Diego; California; USA |
NIGMS GM1077402 | PMID:19022853 PMID:16381841 |
Free, Freely available | nlx_47724, biotools:tcdb | https://bio.tools/tcdb | SCR_004490 | Transporter Classification Database | 2026-02-17 10:00:17 | 311 | ||||
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NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | data access protocol, software application, data processing software, data analysis software, software resource, web service, sequence analysis software | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov https://bio.tools/blast https://sources.debian.org/src/ncbi-blast+/ |
SCR_004870 | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-02-17 10:00:50 | 15381 | ||||
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Philius Resource Report Resource Website |
Philius (RRID:SCR_004625) | Philius | production service resource, analysis service resource, service resource, software resource, data analysis service | Web server that predicts protein transmembrane topology and signal peptides. Hidden Markov models (HMM) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. They expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBN). Their model, Philius, is inspired by a previously published HMM, Phobius, and combines a signal peptide sub-model with a transmembrane sub-model. They introduce a two-stage DBN decoder which combines the power of posterior decoding with the grammar constraints of Viterbi-style decoding. Philius also provides protein type, segment, and topology confidence metrics to aid in the interpretation of the predictions. | hidden markov model, protein type, segment, topology, confidence metric, prediction, protein, transmembrane, signal peptide, peptide, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:18989393 | nlx_62426, biotools:philius | https://bio.tools/philius | SCR_004625 | 2026-02-17 10:00:39 | 0 | |||||||
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PhenoM - Phenomics of yeast Mutants Resource Report Resource Website |
PhenoM - Phenomics of yeast Mutants (RRID:SCR_006970) | PhenoM | data or information resource, production service resource, analysis service resource, database, service resource, image collection, data analysis service | Database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae, it allows storing, retrieving, visualizing and data mining the quantitative single-cell measurements extracted from micrographs of the temperature-sensitive (ts) mutant cells. PhenoM allows users to rapidly search and retrieve raw images and their quantified morphological data for genes of interest. The database also provides several data-mining tools, including a PhenoBlast module for phenotypic comparison between mutant strains and a Gene Ontology module for functional enrichment analysis of gene sets showing similar morphological alterations. About one-fifth of the genes in the budding yeast are essential for haploid viability and cannot be functionally assessed using standard genetic approaches such as gene deletion. To facilitate genetic analysis of essential genes, we and others have assembled collections of yeast strains expressing temperature-sensitive (ts) alleles of essential genes. To explore the phenotypes caused by essential gene mutation we used a panel of genetically engineered fluorescent markers to explore the morphology of cells in the ts strain collection using high-throughput microscopy. The database contains quantitative measurements of 1,909,914 cells and 78,194 morphological images for 775 temperature-sensitive mutants spanning 491 different essential genes in permissive temperature (26* C) and restrictive temperature (32* C). The morphological images were generated by high-content screening (HCS) technology. | phenomics, phenotype, yeast, mutant, cell, morphology, essential gene, gene, high-content screening, microscopy, micrograph, mutant cell, temperature-sensitive allele, allele, genetic analysis, blast, mutation, orf, actin, dna damage, nucleus, mitochondria, plasma membrane, mitotic spindle, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Research Fund ; Fudan University - University of Toronto Exchange Scholarship ; Canadian Institutes of Health Research GMX-201237; Canadian Institutes of Health Research GMX-211012; Canadian Foundation for Innovation LEF-21475 |
PMID:22009677 | Free | nlx_151489, biotools:phenom, r3d100012722 | https://bio.tools/phenom https://doi.org/10.17616/R3GJ5J |
SCR_006970 | Phenomics of yeast Mutants, Phenomics of yeast Mutants (PhenoM) | 2026-02-17 10:01:02 | 0 | ||||
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TriTrypDB Resource Report Resource Website 500+ mentions |
TriTrypDB (RRID:SCR_007043) | TriTrypDB | data access protocol, data or information resource, production service resource, analysis service resource, database, service resource, software resource, web service, data analysis service | An integrated genomic and functional genomic database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ''''User Comments'''' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate. TriTrypDB provides programmatic access to its searches, via REST Web Services. The result of a web service request is a list of records (genes, ESTs, etc) in either XML or JSON format. REST services can be executed in a browser by typing a specific URL. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI). | kinetoplastid parasite, pathogen, genome, gene chromosome, annotation, trypanosomatidae, parasite, blast, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: GeneDB is related to: GeneDB Lmajor is related to: GeneDB Tbrucei has parent organization: Eukaryotic Pathogen Database Resources |
Bill and Melinda Gates Foundation 50097; Wellcome Trust WT085822MA; Wellcome Trust WT085775/Z/08/Z |
PMID:19843604 | Public - please cite. Much of the data in TriTrypDB is provided by independent researchers. Please cite them if you use their data. | nlx_152064, biotools:tritrypdb, r3d100011479 | https://bio.tools/tritrypdb https://doi.org/10.17616/R3J05N |
SCR_007043 | 2026-02-17 10:01:10 | 670 | |||||
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agriGO Resource Report Resource Website 1000+ mentions |
agriGO (RRID:SCR_006989) | agriGO | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | A web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | browser, gene, online tool, visualization, statistical analysis, term enrichment, text mining, ontology or annotation browser, ontology or annotation visualization, database or data warehouse, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: China Agricultural University; Beijing; China |
Ministry of Science and Technology of China 90817006; Ministry of Science and Technology of China 2006CB100105 |
PMID:20435677 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149099, OMICS_02265, biotools:agrigo | https://bio.tools/agrigo | SCR_006989 | agriGO -- GO Analysis Toolkit and Database for Agricultural Community | 2026-02-17 10:01:02 | 1716 | ||||
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IMGT/GENE-DB Resource Report Resource Website 50+ mentions |
IMGT/GENE-DB (RRID:SCR_006964) | IMGT/GENE-DB | narrative resource, international standard specification, data or information resource, database, standard specification | IMGT/GENE-DB is the comprehensive IMGT genome database for immunoglobulin (IG) and T cell receptor (TR) genes from human and mouse, and, in development, from other vertebrates. IMGT/GENE-DB is the international reference for the IG and TR gene nomenclature and works in close collaboration with the HUGO Nomenclature Committee, Mouse Genome Database and genome committees for other species. IMGT/GENE-DB allows a search of IG and TR genes by locus, group and subgroup, which are CLASSIFICATION concepts of IMGT-ONTOLOGY. Short cuts allow the retrieval gene information by gene name or clone name. Direct links with configurable URL give access to information usable by humans or programs. An IMGT/GENE-DB entry displays accurate gene data related to genome (gene localization), allelic polymorphisms (number of alleles, IMGT reference sequences, functionality, etc.) gene expression (known cDNAs), proteins and structures (Protein displays, IMGT Colliers de Perles). It provides internal links to the IMGT sequence databases and to the IMGT Repertoire Web resources, and external links to genome and generalist sequence databases. IMGT/GENE-DB manages the IMGT reference directory used by the IMGT tools for IG and TR gene and allele comparison and assignment, and by the IMGT databases for gene data annotation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: IMGT - the international ImMunoGeneTics information system |
Centre National de la Recherche Scientifique ; Ministere de l'Education Nationale de l'Enseignement Superieur et de la Recherche BIOSTIC-LR2004; Ministere de l'Education Nationale de l'Enseignement Superieur et de la Recherche ACI-IMPBIO IMP82-2004; European Union 5th PCRDT programme QLG2-2000-01287 |
PMID:15608191 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03012, biotools:IMGt_GENE-Db, r3d100012536 | https://bio.tools/IMGT_GENE-DB https://doi.org/10.17616/R3Q48Q |
http://imgt.cines.fr, http://imgt.cines.fr/cgi-bin/GENElect.jv | SCR_006964 | 2026-02-17 10:01:00 | 78 | ||||
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VBASE2 Resource Report Resource Website 50+ mentions |
VBASE2 (RRID:SCR_007082) | VBASE2 | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences. Based on the properties of the source sequences, V genes are classified into 3 different classes: * Class 1: genomic and rearranged evidence * Class 2: genomic evidence only * Class 3: rearranged evidence only This allows careful sequence quality validation by the user. References to other immunological databases ( KABAT, IMGT/LIGM and VBASE ) are given to provide all public annotation data for each V gene. The VBASE2 database can be accessed either by the Direct Query interface or by the DNAPLOT Query interface. The Sequences given by the user are aligned with DNAPLOT against the VBASE2 database. Direct Query allows to enter sequence IDs and names (Field 1), choose species, locus, V gene family and class (Field 2) or search for 100% sequences (Field 3). At the DNAPLOT Query, the sequences given by the user are aligned with DNAPLOT against the VBASE2 database. The DNAPLOT program offers V gene nucleotide sequence alignment referring to the IMGT V gene unique numbering. The Quick Search can be used either for Direct Query to search for sequence IDs and V gene names or for DNAPLOT Query for up to 5 sequences. The new Fab Analysis allows you to align Fab, scFab, scAb or scFv sequences with DNAPLOT against the VBASE2 database, where both heavy and light chain are analyzed. | v gene sequence, v gene, gene, dna, sequence, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: European Nucleotide Archive (ENA) is related to: Ensembl |
BMBF 031U110A/031U210A | PMID:15608286 | Acknowledgement requested | nlx_25238, biotools:germ-line_v_genes | https://bio.tools/germ-line_v_genes | SCR_007082 | VBASE2: the integrative germ-line V gene database | 2026-02-17 10:01:10 | 72 | ||||
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Gene3D Resource Report Resource Website 100+ mentions |
Gene3D (RRID:SCR_007672) | Gene3D | data access protocol, storage service resource, data or information resource, database, service resource, software resource, web service, data repository | A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein domain, protein, protein superfamily, hidden markov model, structural domain, genome, sequence, domain assignments, protein structure, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University College London; London; United Kingdom |
NIH ; Wellcome Trust ; European Union FP6 ENFIN LSHG-CT-2003-503265; European Union FP6 ENFIN LSHG-CT-2004-512092; European Union FP6 ENFIN LSHG-CT-2005-518254; DOE DE-AC02-065CH11357 |
PMID:19906693 PMID:18032434 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02877, biotools:gene3d | https://bio.tools/gene3d | SCR_007672 | Gene3D - Structures assigned to Genomes | 2026-02-17 10:01:16 | 272 | ||||
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Variant Effect Predictor Resource Report Resource Website 1000+ mentions |
Variant Effect Predictor (RRID:SCR_007931) | VEP | production service resource, analysis service resource, service resource, software resource, data analysis service | Data analysis service to predict the functional consequences of known and unknown variants. | perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ensembl |
biotools:ensembl_variant_effect_predictor | https://bio.tools/ensembl_variant_effect_predictor | SCR_007931 | Ve!P | 2026-02-17 10:01:09 | 1871 | |||||||
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Gene Expression Atlas Resource Report Resource Website 100+ mentions |
Gene Expression Atlas (RRID:SCR_007989) | data or information resource, database, expression atlas, atlas | Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. The EBI Gene Expression Atlas Blog discusses ideas, features and problems of creating a large scale meta-analytical atlas of gene expression from publicly available microarray data. Atlas REST API provides all the results available in the main web application in a pragmatic, easy to use form - simple HTTP GET queries as input and either JSON or XML formats as output. Gene Expression Atlas goals: 1. Provision of a statistically robust framework for integration of gene expression experiment results across different platforms at a meta-analytical level 2. A simple interface for identifying strong differential expression candidate genes in conditions of interest 3. Integration of ontologies for high quality annotation of gene and sample attributes 4. Construction of new gene expression summarized views, with a view to analysis of putative signaling pathway targets, discovery of correlated gene expression patterns and the identification of condition/tissue-specific patterns of gene expression. | expression, gene, annotation, assay, molecular neuroanatomy resource, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: ArrayExpress is related to: Experimental Factor Ontology has parent organization: European Bioinformatics Institute |
EMBL ; European Union FELICS ; European Union EMERALD |
nif-0000-06686, biotools:gxa_expt, r3d100010223, biotools:gene_expression_atlas | https://bio.tools/gxa_expt https://bio.tools/gene_expression_atlas https://doi.org/10.17616/R3Z888 |
SCR_007989 | 2026-02-17 10:01:17 | 127 | ||||||||
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eTBlast Resource Report Resource Website 1+ mentions |
eTBlast (RRID:SCR_008188) | eTBlast | data or information resource, narrative resource, database, service resource | eTBLAST is a unique search engine for searching biomedical literature. Our service is very different from PubMed. While PubMed searches for keywords, our search engine lets you input an entire paragraph and returns MEDLINE abstracts that are similar to it. This is something like PubMed''s Related Articles feature, only better because it runs on your unique set of interests. For example, input the abstract of an unpublished paper or a grant proposal into our engine, and with the touch of a button you''ll be able to find every abstract in MEDLINE dealing with your topic. No more guessing whether your set of keywords has found all the right papers. No more sorting through hundreds of papers you don''t care about to find the handful you were looking for--our search engine does it for you. When most people use PubMed to search MEDLINE they pick one or two keywords to describe their topic, then browse through a long list of results. When they find a paper that looks interesting they click on its Related Articles, in hopes of finding more papers like that one. If they find another relevant paper, they explore it''s related articles--and so on. This process of culling long lists of documents by hand makes literature searching tedious and time consuming. We make it easier for you by providing better results the first time, and then allowing you to automatically combine the papers you care about for a second round. Our Iterate feature allows you to checkmark the abstracts you found interesting in the first round and combine them all to create a new query. It''s like rolling several Related Articles lists into one. * We sort our results by relevance, while PubMed sorts by date. * We save you the time and effort of creating a complicated query. * We let you iterate your search over several good papers to narrow your focus. * We provide you the full MEDLINE abstract in our results, and a link to the PubMed page. * We can send your results straight to your email so you never lose a reference or forget where you found it. * This absolutely free service is provided by the University of Texas Southwestern Medical Center. No registration necessary! | biomedical, literature, medline interfaces, paper, publish, search engine, unpublished, journal, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
Hudson Foundation ; P.O'B. Montgomery Distinguished Chair |
PMID:16926219 | biotools:etblast, nif-0000-21148 | https://bio.tools/etblast | http://invention.swmed.edu/etblast/index.shtml | SCR_008188 | eTBLAST: a text-similarity based search engine | 2026-02-17 10:01:06 | 4 | ||||
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tRNAscan-SE Resource Report Resource Website 1000+ mentions |
tRNAscan-SE (RRID:SCR_008637) | web application, production service resource, analysis service resource, service resource, software resource, data analysis service | Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file). | bio.tools, tRNA genes, genomic sequence |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
PMID:15980563 PMID:9023104 DOI:10.1093/nar/25.5.0955 |
Free, Freely available | SCR_010835, OMICS_00385, nif-0000-32031, biotools:trnascan-se | https://bio.tools/trnascan-se https://sources.debian.org/src/trnascan-se/ |
SCR_008637 | Lowe Lab tRNAscan-SE | 2026-02-17 10:01:09 | 2493 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
