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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
PrimerStudio
 
Resource Report
Resource Website
1+ mentions
PrimerStudio (RRID:SCR_008232) data or information resource, database PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu. eukaryotic, exon, gene, amplicon, amplifcation, analysis, dinucleotide, dna, genome, genomic, molecular probe and primer databases, mononucleotide, mutation, organism, pcr, primer, prokaryotic, region, repetitive, segment, sequence, snp, snp detection nif-0000-21334 SCR_008232 PrimerStudio 2026-08-05 10:44:57 1
Microbial Genomics Program
 
Resource Report
Resource Website
1+ mentions
Microbial Genomics Program (RRID:SCR_008140) data or information resource, database Through its Microbial Genome Program (MGP) and its Genomics:GTL (GTL) program, DOEs Office of Biological and Environmental Research (BER) has sequenced more than 485 microbial genomes and 30 microbial communities having specialized biological capabilities. Identifying these genes will help investigators discern how gene activities in whole living systems are orchestrated to solve myriad life challenges. The MGP was begun in 1994 as a spinoff from the Human Genome Program. The goal of the program was to sequence the genomes of a number of nonpathogenic microbes that would be useful in solving DOE''s mission challenges in environmental-waste cleanup, energy production, carbon cycling, and biotechnology. Past projects include microbial genome program, microbial cell project, and the Laboratory Science Program at the DOE Joint Genome Institute. The two ongoing projects are Genomics: GTL program and Community Sequencing Program at the DOE Joint Genome Institute. Sponsors: Site sponsored by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. energy, environmental, gene, biological, biotechnology, carbon, community, cylcling, genome, genomic, living, microbes, microbial, nonpathogenic, system has parent organization: United States Department of Energy THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-20962 SCR_008140 MGP 2026-08-05 10:44:55 2
AnoBase: An Anopheles database
 
Resource Report
Resource Website
1+ mentions
AnoBase: An Anopheles database (RRID:SCR_008166) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 22, 2023. A database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world''''s most important malaria vector. AnoBase is an integrated, relational database of basic biological and genetic data on anopheline species, with a particular emphasis on Anopheles gambiae. It has been designed as an information source and research support tool for the broad vector biology community. Although AnoBase is not a primary genomic database that develops and provides tools to access the genome of the malaria mosquito, it nevertheless contains several sections that offer data of genomic interest such as in situ hybridization images, an integrated gene tool and direct online access to AnoXcel, the proteomic database of An. gambiae. Moreover, AnoBase also contains information on non-gambiae mosquito species and a novel section on studies related to insecticide resistance. gene, genetic, anopheles gambiae, anopheline, biological, biology, community, genomic, in-situ hybridization, insecticide, invertebrate databases, malaria, mosquito, proteomic, specie, vector, image is related to: VectorBase
has parent organization: Foundation for Research and Technology-Hellas; Heraklion; Greece
is parent organization of: Malaria Ontology
NIAID THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21031 http://www.anobase.org/ SCR_008166 AnoBase 2026-08-05 10:44:56 2
Migratory Locust EST Database
 
Resource Report
Resource Website
1+ mentions
Migratory Locust EST Database (RRID:SCR_008201) data or information resource, database The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects. Its transcriptomic data provide invaluable information for molecular entomology study of the insect and pave a way for comparative studies of other medically, agronomically, and ecologically relevant insects. This first transcriptomic database of the locust (LocustDB) has been developed, building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. It currently hosts 45,474 high quality EST sequences from the locust, which were assembled into 12,161 unigenes. This database contains original sequence data, including homologous/orthologous sequences, functional annotations, pathway analysis, and codon usage, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. LocustDB also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. It starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporation of in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies. ecologically, entomology, est, fruitfly, functional, gene, agronomically, analysis, annotation, codon, comparative, data, domain, genomic, hemimetabolous, homologous, honeybee, insect, invertebrate, invertebrate databases, locust, locusta migratoria, medically, migratory, molecular, mosquito, nematode, orthologous, orthopteran, pathway, pest, protein, sequence, silkworm, specie, transcriptome, transcriptomic, unigene, ontology has parent organization: BGI; Shenzhen; China nif-0000-21244 SCR_008201 LocustDB 2026-08-05 10:44:55 7
Plasmid Genome Database
 
Resource Report
Resource Website
10+ mentions
Plasmid Genome Database (RRID:SCR_008228) data or information resource, database The Plasmid Genome Database aims to collate biological and genomic data for all bacterial plasmids in the hopes of enabling rapid, interrogation of both meta- and genomic data. Data maintained includes access to all plasmid genomes and information on core genomic features obtained from parsing the original EMBL/DDBJ/NCBI submission. In addition a suite of third party analyses has been performed for each genome to supplement the original annotation. This site also links to Genome Atlases provided by the Centre for Biological Sequence Analysis (CBS). The motivation behind the construction of this site derived from observations from genome sequencing projects: the abundance and inferred importance of the horizontal gene pool (HGP) in bacterial adaptation and evolution. In so far as plasmids are autonomously replicating, extrachromosomal elements they are a readily identifiable and accessible component of the HGP. Also plasmids have been identified in almost all bacterial divisions, ranging in size from less than 2 kbp to > 1.5 Mbp and as such represent a defined, yet diverse and complex sample of genes in the HGP. element, evolution, extrachromosomal, gene, adaptation, atlas, autonomous, bacterial, biological, division, genome, genomic, hgp, plasmid, pool, prokaryote databases, replicate nif-0000-21323 http://www.genomics.ceh.ac.uk/plasmiddb/ SCR_008228 PGD 2026-08-05 10:44:56 21
Alizadehlab: MeeboChip and HeeboChip Open Source Project
 
Resource Report
Resource Website
1+ mentions
Alizadehlab: MeeboChip and HeeboChip Open Source Project (RRID:SCR_008384) data or information resource, database This is an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and are in the process of building the human counterpart, HEEBOChip. The set of 70mers for MEEBOChip is already available from Illumina, Inc., with synthesis of HEEBOChip 70mers in progress. Both arrays are based on a novel selection of exonic long-oligonucleotides (70-mers) from a genomic annotation of the corresponding complete genome sequences, using a transcriptome-based annotation of exon structure for each genomic locus. Using a combination of existing and custom-tailored tools and datasets (including millions of mRNA and EST sequences), we built and performed a systematic examination of transcript-supported exon structure for each genomic locus at the base-pair level (i.e., exonic evidence). This strategy allowed them to select both constitutive and in many cases alternative exons for nearly every gene in the corresponding genome (e.g., protocadherin locus), allowing an unprecedented exploration of human and mouse biology. Furthermore, they used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, they applied and refined the ArrayOligoSelector algorithm from Joe DeRisis laboratory to select 70mers, considering not only their uniqueness (i.e., hybridization specificity) within the content of the entire genome, but also to overcome the known biases of labeling and hybridization methods (e.g., 3-biased reverse transcription and in vitro transcription reactions). mouse, exonic, evidence, oligonucleotide, chip, human, array, genomic, annoation, sequence, transcriptome, annotation, dataset, mrna, est, systematic, transcript, exon, locus, biology has parent organization: Stanford University; Stanford; California Stanford University ;
UCSF ;
Stowers-Institute ;
Rockefeller University ;
Basel University
nif-0000-30030 SCR_008384 MeeboChip and HeeboChip 2026-08-05 10:45:00 7
GC/GCF
 
Resource Report
Resource Website
1+ mentions
GC/GCF (RRID:SCR_009075) software application, software resource Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software) gene, genetic, genomic, r, linux is listed by: Genetic Analysis Software nlx_154072, SCR_000846, nlx_154584 SCR_009075 R/GCF, R/GC, Genomic Control 2026-08-05 10:45:10 1
SPIKE
 
Resource Report
Resource Website
100+ mentions
SPIKE (RRID:SCR_010466) SPIKE data or information resource, service resource, database Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways visualization, analysis, cellular, signaling pathway, regulatory network, function, genomic, proteomic, cell cycle, dna damage, cell death, stress, transcription factor, mitogen, protein kinase, pathway, immune response, signaling, hearing, dna damage response, programmed cell death, development, ear, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
is related to: ConsensusPathDB
has parent organization: Tel Aviv University; Ramat Aviv; Israel
Cancer A-T Children's Project ;
Wolfson Foundation ;
European Union FP7 ;
Israel Science Foundation
PMID:21097778
PMID:18289391
biotools:spike, nlx_157705 https://bio.tools/spike SCR_010466 Signaling Pathway Integrated Knowledge Engine 2026-08-05 10:45:24 128
COVIBD
 
Resource Report
Resource Website
COVIBD (RRID:SCR_009155) software application, software resource Software application that refines linkage analysis of affected sibpairs by considering attributes or environmental exposures thought to affect disease liability. This refinement utilizes a mixture model in which a disease mutation segregates in only a fraction of the sibships, with the rest of the sibships unlinked. Covariate information is used to predict membership within the two groups corresponding to the linked and unlinked sibships. The pre-clustering model uses covariate information to first form two probabilistic clusters and then tests for excess IBD-sharing in the clusters. The Cov-IBD model determines probabilistic group membership by joint consideration of covariate and IBD values. (entry from Genetic Analysis Software) gene, genetic, genomic, r is listed by: Genetic Analysis Software nlx_154207, nlx_154275, SCR_009109 SCR_009155 R/COVIBD 2026-08-05 10:45:10 0
Genomic HyperBrowser
 
Resource Report
Resource Website
10+ mentions
Genomic HyperBrowser (RRID:SCR_010909) Genomic HyperBrowser data analysis service, production service resource, service resource, analysis 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 2026-08-05 10:45:28 20
Forsyth Institute Bioinformatics Core Facility
 
Resource Report
Resource Website
Forsyth Institute Bioinformatics Core Facility (RRID:SCR_009783) access service resource, service resource, core facility Core specializes in oral microbial genomics, taxonomy, phylogenetics and the next generation sequence (NGS) data analysis with both in house and cloud high performance computational resource. In addition to supporting funded bioinformatics projects, Bioinformatics Core will also provide computational support to Forsyth and other researchers for processing, analyzing, and interpreting biological data. USEDit, ABRF, microarray, data analysis service, microbial, genomic, gene expression, biological data is listed by: Eagle I
is listed by: ABRF CoreMarketplace
has parent organization: Forsyth Institute
open SCR_021784, nlx_156252, ABRF_1234 https://coremarketplace.org/?FacilityID=1234 http://harvard.eagle-i.net/i/0000012e-6d1b-f8ef-55da-381e80000000 SCR_009783 Forsyth Bioinformatics Core, Forsyth Bioinformatics Core Facility 2026-08-05 10:45:15 0
Ontology for Genetic Interval
 
Resource Report
Resource Website
Ontology for Genetic Interval (RRID:SCR_003423) OGI data or information resource, ontology, controlled vocabulary An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure. owl, genomic, genetic, dna, rna, allele, marker, chromosome, rna molecule is listed by: BioPortal
is listed by: OBO
is listed by: Google Code
is related to: Information Artifact Ontology
Free, Available for download, Freely available nlx_157517 https://bioportal.bioontology.org/ontologies/OGI SCR_003423 2026-08-05 10:43:50 0
SOURCE
 
Resource Report
Resource Website
50+ mentions
SOURCE (RRID:SCR_005799) SOURCE data or information resource, database, data analysis service, production service resource, service resource, analysis service resource SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list is listed by: Gene Ontology Tools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: SMD
NIGMS ;
NCI CA85129-04;
NIGMS GM07365
PMID:12519986 Restricted biotools:source, nlx_149287 https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1, https://bio.tools/source SCR_005799 2026-08-05 10:44:21 69
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, nif-0000-03572, biotools:toxodb https://bio.tools/toxodb http://ToxoDB.org SCR_013453 Toxoplasma Genomics Resource, ToxoDB 2026-08-05 10:46:02 137
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 2026-08-05 10:46:54 5
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 2026-08-05 10:43:06 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 2026-08-05 10:43:09 3
HOMOZYGOSITYMAPPER
 
Resource Report
Resource Website
100+ mentions
HOMOZYGOSITYMAPPER (RRID:SCR_001714) HomozygosityMapper data analysis service, production service resource, service resource, analysis 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 2026-08-05 10:43:26 121
ACGT Inc.
 
Resource Report
Resource Website
ACGT Inc. (RRID:SCR_001026) ACGT production service resource, service resource, analysis 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 2026-08-05 10:43:17 0
Phevor
 
Resource Report
Resource Website
1+ mentions
Phevor (RRID:SCR_002273) Phevor data analysis service, production service resource, service resource, analysis 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 2026-08-05 10:43:37 9

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