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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Xenbase Resource Report Resource Website 100+ mentions |
Xenbase (RRID:SCR_003280) | XenBase | storage service resource, service resource, data repository, data or information resource, image repository, database | Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics. | molecular neuroanatomy resource, dna target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, blast, development stage, publication, in situ hybridization, immunohistochemistry, video resource, organism-related portal, experimental protocol, organism supplier, data analysis service, developmental stage, gold standard, bio.tools, FASEB list, RRID Community Authority |
is listed by: OMICtools is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of Calgary; Alberta; Canada is parent organization of: Xenopus Anatomy Ontology |
NICHD R01 HD045776; NICHD P41 HD064556 |
PMID:23125366 PMID:19884130 PMID:36755307 |
Free, Available for download, Freely available | biotools:xenbase, OMICS_01665, nif-0000-01286, r3d100010279 | http://www.xenbase.org/entry/, https://bio.tools/xenbase, https://doi.org/10.17616/R3MP4S | SCR_003280 | Xenbase: Xenopus laevis and tropicalis biology and genomics resource | 2026-08-06 09:25:50 | 446 | ||||
|
PLANTTFDB Resource Report Resource Website 1000+ mentions |
PLANTTFDB (RRID:SCR_003362) | PlantTFDB | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors | transcription factor, expression, regulation, interaction, conserved element, phenotype, function, evolution, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Database of Poplar Transcription Factors is related to: Plant Ontology has parent organization: Peking University; Beijing; China |
China 863 ; China 973 ; NSFC ; China NSFC |
PMID:24174544 PMID:17933783 PMID:21097470 |
Free, Available for download, Freely available | nif-0000-03311, biotools:planttfdb_2.0, OMICS_00560, r3d100010137 | https://bio.tools/planttfdb_2.0, https://doi.org/10.17616/R3JG6V | http://planttfdb.cbi.pku.edu.cn | SCR_003362 | , PlantTFDB 2.0, Plant Transcription Factor Database | 2026-08-06 09:25:52 | 1109 | |||
|
genomation Resource Report Resource Website 50+ mentions |
genomation (RRID:SCR_003435) | genomation | software resource, data analysis software, software toolkit, data processing software, software application | Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters. | genome, genomic interval, genomic feature analysis, GRanges objects, annotate given regions, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:25417204 | Free, Available for download, Freely available | biotools:genomation, OMICS_02306 | https://github.com/al2na/genomation, https://github.com/BIMSBbioinfo/genomation, https://bio.tools/genomation | http://al2na.github.io/genomation/ | SCR_003435 | 2026-08-06 09:25:53 | 58 | |||||
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NeuroMatic Resource Report Resource Website 100+ mentions |
NeuroMatic (RRID:SCR_004186) | data analysis software, software application, software resource, data processing software | NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into Sets and Groups, NeuroMatic makes it relatively easy to compute transformations and statistical analyses on their data, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, rise-time computations, etc. Being open source and modular designed, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Note, if you have reached this page in search of a freeware tool for neuronal reconstructions, you are more likely to be interested in Neuromantic, a software package that sounds like NeuroMatic, but is not quite the same. Features of NeuroMatic Include * Sorting, Scaling, Averaging, Interpolation * Max / Min / Mean / Level / Rise Time / FWHM / Slope Measurements * Stability / Stationarity Analysis * Event Detection * Waveform Template Matching * Spike Raster Plots * Interspike-Interval and Peri-Stimulus Time (PST) Histograms * Compact Easy-to-Use Interface * Modular design as a basis for your own procedures * Extra space for your own buttons and controls * Import functions for Axograph and Pclamp data * Automatic macro generation for batch processing Supporting Agencies: MRC, Wellcome Trust Spike, Event, Fit, NClamp, Acquisition, spike train, EPSP, IPSP, IPSC, EPSC | epsc, epsp, event, fit, acquisition, data management, ipsc, ipsp, nclamp, software, spike, spike train, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University College London; London; United Kingdom |
PMID:29670519 | nif-0000-00073, biotools:neuromatic | https://bio.tools/neuromatic | SCR_004186 | NeuroMatic | 2026-08-06 09:26:03 | 301 | |||||||
|
MRtrix Resource Report Resource Website 100+ mentions |
MRtrix (RRID:SCR_006971) | MRtrix | source code, software resource, software toolkit, data processing software, software application | A set of tools to perform diffusion-weighted MRI white matter tractography in the presence of crossing fibres, using Constrained Spherical Deconvolution (Tournier et al.. 2004; Tournier et al. 2007), and a probabilisitic streamlines algorithm (e.g. Behrens et al., 2003; Parker et al., 2003). These applications have been written from scratch in C++, using the functionality provided by the GNU Scientific Library, and gtkmm. The software is currently capable of handling DICOM, NIfTI and AnalyseAVW image formats, amongst others. Installation * Unix/Linux * Microsoft Windows * Mac Os X, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | white matter tractography, diffusion mri, tractography, fiber tracking, crossing fiber, constrained spherical deconvolution, diffusion mr fiber tracking, image display, dti, linux, c++, analyze, bshort, bfloat, dicom, nifti-1, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: Diffusion MRI of Traumatic Brain Injury is related to: neurodebian has parent organization: Florey Institute of Neuroscience and Mental Health; Victoria; Australia |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153918 | http://www.nitrc.org/projects/mrtrix/, https://sources.debian.org/src/mrtrix/ | SCR_006971 | 2026-08-06 09:26:45 | 205 | |||||||
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PhenoM - Phenomics of yeast Mutants Resource Report Resource Website |
PhenoM - Phenomics of yeast Mutants (RRID:SCR_006970) | PhenoM | service resource, production service resource, data analysis service, data or information resource, image collection, analysis service resource, database | 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) | 2026-08-06 09:26:43 | 0 | ||||
|
eXpress Resource Report Resource Website 100+ mentions |
eXpress (RRID:SCR_006873) | eXpress | sequence analysis software, software resource, data analysis software, data processing software, software application |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018. From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/. Software for streaming quantification for high-throughput DNA/RNA sequencing. Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them. |
quantification, high-throughput, DNA, RNA, sequencing, target, fragment, analysis |
is listed by: OMICtools is listed by: Debian has parent organization: University of California at Berkeley; Berkeley; USA |
NSF ; NHGRI R01HG006129 |
DOI:10.1038/nmeth.2251 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015990, OMICS_01275 | https://sources.debian.org/src/berkeley-express/ | SCR_006873 | eXpress - Streaming quantification for high-throughput sequencing, Berkeley-express | 2026-08-06 09:26:41 | 494 | ||||
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agriGO Resource Report Resource Website 1000+ mentions |
agriGO (RRID:SCR_006989) | agriGO | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | 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 | 2026-08-06 09:26:43 | 1716 | ||||
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PrimerBank Resource Report Resource Website 1000+ mentions |
PrimerBank (RRID:SCR_006898) | PrimerBank | storage service resource, service resource, data repository, data or information resource, database | Database of human and mouse primer pairs for gene expression analysis by polymerase chain reaction (PCR) and quantitative PCR (qPCR). A total of 306,800 primers covering most known human and mouse genes can be accessed from the PrimerBank database, together with information on these primers such as T(m), location on the transcript and amplicon size. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. All primers in PrimerBank were carefully designed to ensure gene specificity. All experimental validation data for mouse primers are available from PrimerBank. You can submit your primers. They will be added to the database once they are properly QCd. | electrophoresis, gene expression, quantitative pcr, gel, gene, agarose, algorithm, amplification, human, molecular probe, primer database, mouse, pcr, primer, primer pair, protein, quantification, reaction, secondary structure, polymerase chain reaction, real-time pcr, pcr primer, detection, blast, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Harvard Medical School; Massachusetts; USA |
NHLBI U01 HL66678 | PMID:22086960 PMID:19906719 PMID:19108745 PMID:14654707 |
Public, Acknowledgement requested, The community can contribute to this resource | nif-0000-21333, OMICS_02323, biotools:primerbank | https://bio.tools/primerbank | SCR_006898 | PrimerBank: PCR Primers for Gene Expression Detection and Quantification | 2026-08-06 09:26:43 | 1577 | ||||
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IMGT/GENE-DB Resource Report Resource Website 50+ mentions |
IMGT/GENE-DB (RRID:SCR_006964) | IMGT/GENE-DB | international standard specification, data or information resource, standard specification, narrative resource, database | 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 | 2026-08-06 09:26:43 | 78 | ||||
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BOXSHADE 3.21 Resource Report Resource Website 500+ mentions |
BOXSHADE 3.21 (RRID:SCR_007165) | portal, topical portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. This server takes a multiple-alignment file in either GCG''s MSF-format or Clustals ALN-format. Sponsors: This resource was supported by the Swiss EMBnet Node Server. Keywords: Server, Multiple-alignment,, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_19792, nif-0000-30211 | https://sources.debian.org/src/boxshade/ | SCR_007165 | BOXSHADE | 2026-08-06 09:26:46 | 599 | ||||||||
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TriTrypDB Resource Report Resource Website 500+ mentions |
TriTrypDB (RRID:SCR_007043) | TriTrypDB | software resource, service resource, data access protocol, production service resource, data analysis service, data or information resource, web service, analysis service resource, database | 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 | 2026-08-06 09:26:44 | 670 | |||||
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VBASE2 Resource Report Resource Website 50+ mentions |
VBASE2 (RRID:SCR_007082) | VBASE2 | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | 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 | 2026-08-06 09:26:44 | 72 | ||||
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DICOMscope Resource Report Resource Website |
DICOMscope (RRID:SCR_007344) | data visualization software, software application, software resource, data processing software | DICOMscope is a free DICOM viewer which can display uncompressed, monochrome DICOM images from all modalities and which supports monitor calibration according to DICOM part 14 as well as presentation states. The application is rather a feasibility study for DICOM presentation states. DICOMscope offers a print client (DICOM Basic Grayscale Print Management) which also implements the optional Presentation LUT SOP Class. | image, data visualization | is listed by: Debian | nif-0000-00287 | https://sources.debian.org/src/dicomscope/ | SCR_007344 | 2026-08-06 09:26:49 | 0 | |||||||||
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Gene3D Resource Report Resource Website 100+ mentions |
Gene3D (RRID:SCR_007672) | Gene3D | storage service resource, software resource, service resource, data access protocol, data repository, data or information resource, web service, database | 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 | 2026-08-06 09:26:55 | 272 | ||||
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ALTree Resource Report Resource Website 1+ mentions |
ALTree (RRID:SCR_007562) | data analysis software, software application, software resource, data processing software | Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci. | phylogeny based association, association detection, susceptibility sites, haplotype phylogenetic trees, gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: Debian |
PMID:16595555 DOI:10.1093/bioinformatics/btl131 |
Free, Available for download, Freely available | OMICS_13032, nlx_154221 | https://sources.debian.org/src/altree/, https://gitlab.inria.fr/NGS/ALTree, | SCR_007562 | ALTREE | 2026-08-06 09:26:53 | 3 | ||||||
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Gene Expression Atlas Resource Report Resource Website 100+ mentions |
Gene Expression Atlas (RRID:SCR_007989) | expression atlas, database, data or information resource, 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 | 2026-08-06 09:27:03 | 127 | ||||||||
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Variant Effect Predictor Resource Report Resource Website 1000+ mentions |
Variant Effect Predictor (RRID:SCR_007931) | VEP | software resource, service resource, production service resource, data analysis service, analysis service resource | 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 | 2026-08-06 09:27:02 | 1871 | |||||||
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eTBlast Resource Report Resource Website 1+ mentions |
eTBlast (RRID:SCR_008188) | eTBlast | service resource, narrative resource, database, data or information 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 | 2026-08-06 09:27:08 | 4 | ||||
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Network Analysis, Visualization and Graphing TORonto Resource Report Resource Website 50+ mentions |
Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) | NAViGaTOR | software resource, d visualization software, data processing software, data visualization software, software application | A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches. | fly, algorithm, capacity, graphical, graphing, human, interaction, interactome, intersection, mouse, network, node, protein, proteomic, rat, worm, yeast, graphing application, 2d visualization, 3d visualization, visualization, biological network, protein-protein interaction, gene, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Genomics Institute ; Canada Research Chair Program ; Ontario Research Fund Research Excellence ; Canada Foundation for Innovation 12301; Canada Foundation for Innovation 203383 |
PMID:19837718 | Freely-downloadable for academic and not-for-profit institutions | nif-0000-25610, biotools:navigator | https://bio.tools/navigator | SCR_008373 | NAViGaTOR - Network Analysis Visualization and Graphing TORonto, NAViGaTOR - Network Analysis Visualization & Graphing TORonto | 2026-08-06 09:27:08 | 52 |
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