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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Toolbox at the European Bioinformatics Institute
 
Resource Report
Resource Website
50+ mentions
Toolbox at the European Bioinformatics Institute (RRID:SCR_002872) software resource, software toolkit The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics. These are subdivided into categories in the left menu for convenience. EBI has developed a large number of very useful bioinformatics tools. A few examples include: - Similarity & Homology - the BLAST or FASTA programs can be used to look for sequence similarity and infer homology. - Protein Functional Analysis - InterProScan can be used to search for motifs in your protein sequence. - Proteomic Services NEW - UniProt DAS server allows researchers to show their research results in the context of UniProtKB/Swiss-Prot annotation. - Sequence Analysis - ClustalW2 a sequence alignment tool. - Structural Analysis - MSDfold can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB). - Web Services - provide programmatic access to the various databases and retrieval/analysis services EBI provides. - Tools Miscellaneous - Expression Profiler a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Sponsors: This resource is sponsored by EBI. expression, functional, gene, bioinformatics, database, genomic, homology, protein, proteomic, sequence, structural, toolbox has parent organization: European Bioinformatics Institute Free nif-0000-25553 SCR_002872 EBI Bioinformatics Tools 2026-09-05 06:32:28 92
GS-EM
 
Resource Report
Resource Website
GS-EM (RRID:SCR_003992) GS-EM software application, software resource Software application (entry from Genetic Analysis Software) gene, genetic, genomic is listed by: Genetic Analysis Software nlx_154366 SCR_003992 GenoSpectrum Expectation-Maximuzation 2026-09-05 06:32:32 0
Platypus
 
Resource Report
Resource Website
100+ mentions
Platypus (RRID:SCR_005389) software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool designed for efficient and accurate variant detection in high throughput sequencing data. Haplotype based variant caller for next generation sequence data. Haplotype based variant caller, next generation sequence data, gene, genomic, high throughput sequencing data, is listed by: OMICtools
is related to: SAMTOOLS
has parent organization: Wellcome Trust Centre for Human Genetics
THIS RESOURCE IS NO LONGER IN SERVICE SCR_009046, nlx_154021, OMICS_00068 SCR_005389 Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data, PLAYPUS 2026-09-05 06:32:35 200
TDTPOWER
 
Resource Report
Resource Website
TDTPOWER (RRID:SCR_005021) TDTPOWER software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that calculates the sample size required for obtaining a prescribed power against a specified alternative for TDT. (entry from Genetic Analysis Software) gene, genetic, genomic, sas macro is listed by: Genetic Analysis Software THIS RESOURCE IS NO LONGER IN SERVICE nlx_154678 SCR_005021 2026-09-05 06:32:34 0
POPDIST
 
Resource Report
Resource Website
POPDIST (RRID:SCR_004904) POPDIST software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures (entry from Genetic Analysis Software) gene, genetic, genomic, unix, (aix/irix/decalpha), linux, macos, ms-dos, ms-windows, (95) is listed by: Genetic Analysis Software PMID:21564908 THIS RESOURCE IS NO LONGER IN SERVICE nlx_154542 SCR_004904 2026-09-05 06:32:34 0
Phevor
 
Resource Report
Resource Website
1+ mentions
Phevor (RRID:SCR_002273) Phevor analysis service resource, data analysis service, production service resource, service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles. genome interpretation, variant prioritization, disease gene prioritization, phenotype, gene function, disease, genomic, disease-causing allele, gene, function, allele has parent organization: University of Utah School of Medicine; Utah; USA PMID:24702956 THIS RESOURCE IS NO LONGER IN SERVICE SciRes_000139 SCR_002273 Phenotype Driven Variant Ontological Re-Ranking Tool 2026-09-05 06:31:17 9
AceView
 
Resource Report
Resource Website
100+ mentions
AceView (RRID:SCR_002277) AceView/WormGenes data or information resource, database 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 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions. est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standard has parent organization: NCBI THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21007, r3d100010651 https://doi.org/10.17616/R3260G http://www.ncbi.nih.gov/IEB/Research/Acembly/ SCR_002277 AceView genes, AceView/WormGenes, The AceView Genes 2026-09-05 06:31:17 186
DogMap
 
Resource Report
Resource Website
DogMap (RRID:SCR_002332) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An international collaboration between 46 labs from 20 different countries towards a low resolution canine marker map under the auspices of the International Society for Animal Genetics (ISAG). The map under development should achieve a resolution of about 20 cM and some of the markers should be mapped physically. The participants have agreed to use microsatellites as markers on a common panel of reference families which will provide the backbone of the marker map. It is foreseen to also include type I markers in the mapping effort and to produce cosmid derived microsatellites for physical mapping. For this purpose part of the effort focuses on the standardization of the canine karyotype. Special attention is payed to hereditary diseases where efforts are under way to establish resource families either by collecting families or by specific breeding. A point of emphasis of the DogMap project is the setting up of an internationally accessible database for handling the mapping data. The structure of the DogMap collaboration includes a managing committee and scientific advisers. The managing committee is responsible for the overall coordination of the activities within the collaboration, for the dissemination of relevant information to all of the participants and for the representation of DogMap outside the collaboration., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. family, genetic, animal, breeding, canine, development, disease, dog, genomic, hereditary, karyotype, map, mapping, marker, microsatellite, model organisms and comparative genomics databases, physical has parent organization: University of Basel; Basel; Switzerland THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21123 SCR_002332 DogMap 2026-09-05 06:31:17 0
Full-Malaria: Malaria Full-Length cDNA Database
 
Resource Report
Resource Website
1+ mentions
Full-Malaria: Malaria Full-Length cDNA Database (RRID:SCR_002348) data or information resource, database FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan. drug, eukaryotic, expression, function, gene, alignment, amino acid, cdna, chromosome, clone, coding, comparative, genome, genomic, human, malaria, medical, nucleotide, oligo-capping, organism, parasite, pathogen, physical, plasmodium falciparum, promoter, protein, region, sequence, sequencing, unicellular eukaryote genome databases, vaccine has parent organization: University of Tokyo; Tokyo; Japan PMID:18987005
PMID:14681428
nif-0000-21157 SCR_002348 Full-Malaria 2026-09-05 06:31:17 2
Ancestrymap
 
Resource Report
Resource Website
10+ mentions
Ancestrymap (RRID:SCR_004353) ANCESTRYMAP software application, software resource, source code Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: bio.tools
has parent organization: Harvard Medical School; Massachusetts; USA
Burroughs Wellcome Fund ;
NHGRI K-01 HG002758-01
PMID:15088269 Restricted nlx_39116, biotools:ancestrymap, OMICS_02083 https://reich.hms.harvard.edu/software, https://bio.tools/ancestrymap http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html SCR_004353 2026-09-05 06:31:24 12
SGN
 
Resource Report
Resource Website
1000+ mentions
SGN (RRID:SCR_004933) SGN, SGN ref data or information resource, database A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions. database, clade, genomic, sequence, phenotype, pathway, genetic, taxonomy, annotation, blast, plant genome, bio.tools, FASEB list is used by: NIF Data Federation
is listed by: bio.tools
is listed by: Debian
is related to: Sol Genomics Network - Bulk download
is related to: AmiGO
has parent organization: Boyce Thompson Institute for Plant Research
USDA ;
ATC Inc. Advanced Technologies Cambridge ;
NSF 0116076;
NSF 9872617;
NSF 975866;
NSF 0421634
PMID:20935049
PMID:16010005
Public, The community can contribute to this resource r3d100012078, nlx_89764, biotools:sol_genomics_network https://bio.tools/sol_genomics_network, https://doi.org/10.17616/R3FS95 http://www.sgn.cornell.edu/ SCR_004933 SGN ref, Sol Genomics Network 2026-09-05 06:31:27 1261
Genomic HyperBrowser
 
Resource Report
Resource Website
10+ mentions
Genomic HyperBrowser (RRID:SCR_010909) Genomic HyperBrowser analysis service resource, data analysis service, production service resource, service resource A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets. genomic, genomic track, gene regulation, disease association, epigenetic modification, genome is listed by: OMICtools
has parent organization: University of Oslo; Oslo; Norway
PMID:23632163
PMID:21182759
OMICS_00638 SCR_010909 The Genomic HyperBrowser 2026-09-05 06:32:00 20
ApiDB ToxoDB
 
Resource Report
Resource Website
100+ mentions
ApiDB ToxoDB (RRID:SCR_013453) ApiDB ToxoDB data or information resource, database A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info end-sequencing, bac clone, data mining tool, microarray, proteomic sequencing, toxoplasma gondii, bac clone, 8x random shotgun, genomic sequencing project, snp, qtl, sequencing, genomic, non-vertebrate, unicellular, eukaryote, genome, pathogen, toxoplasmosis, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: Eukaryotic Pathogen Database Resources
NIAID contract HHSN266200400037C PMID:18003657
PMID:12519989
r3d100012266, biotools:toxodb, nif-0000-03572 https://bio.tools/toxodb http://ToxoDB.org SCR_013453 Toxoplasma Genomics Resource, ToxoDB 2026-09-05 06:32:07 153
Genes, Genome Features and Maps
 
Resource Report
Resource Website
1+ mentions
Genes, Genome Features and Maps (RRID:SCR_017524) data or information resource, database Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models. Data, mouse, gene, DNA, segment, cytogenetic, marker, MGI, genome, feature, sequenced, genomic, map, expression, disease, model Free, Freely available SCR_017524 2026-09-05 06:32:15 6
ENTROPY BLOCKER
 
Resource Report
Resource Website
ENTROPY BLOCKER (RRID:SCR_000123) ENTROPY BLOCKER software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software) gene, genetic, genomic, r, ms-windows, linux is listed by: Genetic Analysis Software THIS RESOURCE IS NO LONGER IN SERVICE nlx_154300, nlx_154581, SCR_007247 SCR_000123 R/ENTROPY BLOCKER, R/ENTROPY_BLOCKER 2026-09-05 06:31:09 0
dbSTS
 
Resource Report
Resource Website
1+ mentions
dbSTS (RRID:SCR_000400) dbSTS data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences. genomic, mapping, sequence, gold standard, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: NCBI
NIH PMID:2781285 THIS RESOURCE IS NO LONGER IN SERVICE biotools:dbsts, nif-0000-20939, r3d100010649 https://bio.tools/dbsts, https://doi.org/10.17616/R39P5C SCR_000400 NCBI dbSTS: database of Sequence Tagged Sites, Sequence Tagged Sites Database, NCBI dbSTS, dbSTS: database of Sequence Tagged Sites, Database of Sequence Tagged Sites 2026-09-05 06:31:10 3
ACGT Inc.
 
Resource Report
Resource Website
ACGT Inc. (RRID:SCR_001026) ACGT analysis service resource, production service resource, service resource Company which provides a suite of molecular biology and genomic services, including DNA sequencing by Sanger and Next Generation Sequencing. All services are offered at a research, GLP or clinical grade levels. commercial, molecular biology, bioinformatics, genomic, service, dna sequencing is listed by: ScienceExchange Restricted SciEx_10623 http://www.scienceexchange.com/facilities/acgt-inc SCR_001026 2026-09-05 06:31:13 0
HOMOZYGOSITYMAPPER
 
Resource Report
Resource Website
100+ mentions
HOMOZYGOSITYMAPPER (RRID:SCR_001714) HomozygosityMapper analysis service resource, data analysis service, production service resource, service resource A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software) gene, genetic, genomic, perl, genotype, homozygosity score, homozygosity, bio.tools, FASEB list is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany
PMID:19465395 Free, Freely Available nlx_154069, biotools:homozygositymapper, OMICS_00123 https://bio.tools/homozygositymapper SCR_001714 2026-09-05 06:31:14 125
MADELINE
 
Resource Report
Resource Website
1+ mentions
MADELINE (RRID:SCR_001979) MADELINE service resource, software application, software resource Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review. gene, genetic, genomic, c, unix, solaris, freebsd, openbsd, macos, ms-windows, cygwin, linux, pedigree, draw, linkage association, family association is listed by: OMICtools
is listed by: Genetic Analysis Software
has parent organization: University of Michigan; Ann Arbor; USA
PMID:17488757 THIS RESOURCE IS NO LONGER IN SERVICE nlx_154446, OMICS_00210 http://eyegene.ophthy.med.umich.edu/#madeline SCR_001979 Madeline 2026-09-05 06:31:15 5
HAPLOCLUSTERS
 
Resource Report
Resource Website
HAPLOCLUSTERS (RRID:SCR_007439) HAPLOCLUSTERS software application, software resource Software program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. (entry from Genetic Analysis Software) gene, genetic, genomic, bio.tools is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
Aging nlx_154014, biotools:haploclusters https://bio.tools/haploclusters SCR_007439 2026-09-05 06:32:39 0

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