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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
Genetic and Rare Diseases Information Center
 
Resource Report
Resource Website
10+ mentions
Genetic and Rare Diseases Information Center (RRID:SCR_008695) GARD topical portal, data or information resource, portal, disease-related portal Genetic and Rare Diseases Information Center (GARD) is a collaborative effort of two agencies of the National Institutes of Health, The Office of Rare Diseases Research (ORDR) and the National Human Genome Research Institute (NHGRI) to help people find useful information about genetic conditions and rare diseases. GARD provides timely access to experienced information specialists who can furnish current and accurate information about genetic and rare diseases. So far, GARD has responded to 27,635 inquiries on about 7,147 rare and genetic diseases. Requests come not only from patients and their families, but also from physicians, nurses and other health-care professionals. GARD also has proved useful to genetic counselors, occupational and physical therapists, social workers, and teachers who work with people with a genetic or rare disease. Even scientists who are studying a genetic or rare disease and who need information for their research have contacted GARD, as have people who are taking part in a clinical study. Community leaders looking to help people find resources for those with genetic or rare diseases and advocacy groups who want up-to-date disease information for their members have contacted GARD. And members of the media who are writing stories about genetic or rare diseases have found the information GARD has on hand useful, accurate and complete. GARD has information on: :- What is known about a genetic or rare disease. :- What research studies are being conducted. :- What genetic testing and genetic services are available. :- Which advocacy groups to contact for a specific genetic or rare disease. :- What has been written recently about a genetic or rare disease in medical journals. GARD information specialists get their information from: :- NIH resources. :- Medical textbooks. :- Journal articles. :- Web sites. :- Advocacy groups, and their literature and services. :- Medical databases. genetic, disease, information, genome, human, rare disease, health, physician, counselor, gene, journal, medical has parent organization: National Institutes of Health Office of Rare Diseases Research ;
NHGRI
nif-0000-37627 SCR_008695 Genetic Rare Diseases Information Center 2026-07-30 09:27:58 14
NovoAlign
 
Resource Report
Resource Website
500+ mentions
NovoAlign (RRID:SCR_014818) data processing software, sequence analysis software, data analysis software, software resource, software application Software tool designed for mapping short reads onto a reference genome generated from Illumina, Ion Torrent, and 454 NGS platforms. Its features include paired end alignment, methylation status analysis, automatic base quality calibration, and in built adapter trimming and base quality trimming. sequence analysis software, short read, map, genome, illumina, ion torrent, 454 ngs Commercially available, Trial available by request SCR_014818 2026-07-30 09:29:25 787
SNP2TFBS
 
Resource Report
Resource Website
1+ mentions
SNP2TFBS (RRID:SCR_016885) SNP2TFBS data access protocol, software resource, web service, data or information resource, database Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs. collection, regulatory, single, polymorphism, SNP, affecting, predicted, transcription, factor, binding, site, affinity, data, human, nucleotide, genome Swiss National Science Foundation ;
Swiss Institute of Bioinformatics
PMID:27899579 Free, Freely available SCR_016885 Single Nucleotide Polymorphisms 2 Transcription Factor Binding Site, SNP2TFBS 2026-07-30 09:30:13 7
Diploidocus
 
Resource Report
Resource Website
1+ mentions
Diploidocus (RRID:SCR_021231) data processing software, sequence analysis software, software toolkit, data analysis software, software resource, software application Software package for diploid genome assembly analysis. Sequence analysis toolkit for number of different analyses related to diploid genome assembly. Diploid genome assembly analysis, genome, genome assembly, sequence analysis uses: DepthSizer Free, Available for download, Freely available SCR_021231 2026-07-30 09:30:43 3
University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility
 
Resource Report
Resource Website
University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility (RRID:SCR_017177) University of Manitoba BIT Core Facility core facility, service resource, access service resource, data analysis service, software resource, data or information resource, production service resource, analysis service resource BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management. bioinformatics, genome, assembly, microarray, transcriptomics, pathway, data, analysis, management Restricted SCR_017177 University of Manitoba, BIT, Bio Information Technologies Lab, Fritensky Lab, Canada, Department of Plant Science 2026-07-30 09:30:17 0
LTRpred
 
Resource Report
Resource Website
1+ mentions
LTRpred (RRID:SCR_017031) data processing software, data analytics software, data analysis software, software resource, software application Software package for automated functional annotation of LTR retrotransposons for comparative genomics studies. Used to perform de novo functional annotation of LTR retrotransposons from any genome assembly in fasta format. LTR, retrotransposon, prediction, genome, assembly, functional, annotation is related to: R Project for Statistical Computing Free, Available to download, Freely available https://hajkd.github.io/LTRpred/ SCR_017031 LTRpred(ict) 2026-07-30 09:30:08 6
Sequence Tag Alignment and Consensus Knowledgebase Database
 
Resource Report
Resource Website
Sequence Tag Alignment and Consensus Knowledgebase Database (RRID:SCR_002156) data processing software, software application, data visualization software, software resource, data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index exonic, expressed, expressed sequence tag (est), expression, fragment, gene, alignment, alternative gene, cdna, clone, cluster, developmental, disease, diversity, genome, homo sapiens, human, isoform, knowledgebase, meta-cluster, mrna, pathological, sequence, tissue, transcript, variant, visualization PMID:11125101 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-20946 SCR_002156 STACKdb 2026-07-30 09:26:23 0
UK Sheep Genome Mapping Project
 
Resource Report
Resource Website
1+ mentions
UK Sheep Genome Mapping Project (RRID:SCR_002272) topical portal, data or information resource, database, portal THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The project aims to apply genome mapping research to sheep, utilizing previous research in sheep (in other countries) and in other species (in the UK and abroad) to the benefit of the UK sheep industry. The project itself uses existing breeding structures, knowledge of the sheep genome and experimental resources. It has three main aims: i) To use the Suffolk, Texel and Charollais Sire Referencing Schemes to detect and verify quantitative trait loci (QTLs) for growth and carcass composition traits ii) To investigate candidate genes and/or chromosomal regions for associations with production traits. iii) To investigate approaches for optimizing future genotyping strategies within the sire referencing schemes for practical and cost effective application of marker-assisted selection By using commercial breeding populations for the research, immediate application of beneficial results is possible. Potential benefits include increased genetic progress through marker assisted selection which utilizes the genotype information, correction of possible parentage errors (ultimately leading to additional genetic progress) and opportunities for using marker information for product certification. The project will benefit the UK sheep industry by the use of Marker Assisted Selection (MAS) utilizing QTL or gene variants identified in the project. Additional benefits may arise from parentage verification and correction of errors e.g. misallocation of lamb to ewe. In the longer term, opportunities may exist to use markers for quality control, tracing products to their source. The major advantage of the design of this project is that the results are immediately applicable to the breeding schemes within which the QTLs and/or genes are detected. The time lag in the application of the results that is often seen with experimental populations is minimized. The project requires close involvement with the Sire Reference Schemes, in return for their assistance the results have immediate benefit to animals within these groups. gene, animal, breed, breeding, chromosomal, chromosome, genome, genotype, genotyping, lamb, map, mapping, marker, population, production, region, sheep, specie, structure, trait THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-20995 SCR_002272 UKSGMP 2026-07-30 09:26:25 1
GRS
 
Resource Report
Resource Website
1+ mentions
GRS (RRID:SCR_001008) data processing software, data management software, data analysis software, software resource, software application A compression tool for efficient storage of Genome Re-Sequencing data. GRS processes genome sequence data without use of reference SNPs and other variants. It can also automatically rebuild the individual genome sequence data using the reference genome sequence. data analysis software, data management software, compression tool, data compression, storage, genome, resequencing is listed by: OMICtools THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00960 SCR_001008 2026-07-30 09:26:07 2
NTAP
 
Resource Report
Resource Website
10+ mentions
NTAP (RRID:SCR_001488) NTAP data processing software, software application, data analysis software, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl. software, tiling array, data analysis, rice, arabidopsis, hy5, transcription factor, genome is listed by: OMICtools
has parent organization: Peking University; Beijing; China
PMID:19468055 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00808 SCR_001488 NimbleGen Tiling array Analysis Package, NimbleGen Tilingarray Analysis Package 2026-07-30 09:26:10 10
SoyBase
 
Resource Report
Resource Website
500+ mentions
SoyBase (RRID:SCR_005096) SoyBase service resource, data repository, data analysis service, storage service resource, ontology, controlled vocabulary, data or information resource, database, production service resource, analysis service resource Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome. soybean, gene, genetic map, genome, data set, trait, phenotype, molecular biology, sequence, chromosome, quantitative trait locus, php, genetics, genomics, legume, bio.tools, FASEB list is listed by: 3DVC
is listed by: re3data.org
is listed by: Debian
is listed by: bio.tools
has parent organization: Iowa State University; Iowa; USA
is parent organization of: Soybean Ontologies
is parent organization of: Soy Ontology
USDA Agricultural Research Service PMID:20008513 The community can contribute to this resource nif-0000-03483, r3d100010846, biotools:soybase https://bio.tools/soybase, https://doi.org/10.17616/R3S032 SCR_005096 SoyBase and the Soybean Breeder''s Toolbox, SoyBase and the Soybean Breeder''s Toolbox: Integrating Genetics and Molecular Biology for Soybean Researchers 2026-07-30 09:27:09 646
Pathosystems Resource Integration Center
 
Resource Report
Resource Website
1000+ mentions
Pathosystems Resource Integration Center (RRID:SCR_004154) PATRIC service resource, data analysis service, bioinformatics resource center, data or information resource, database, production service resource, analysis service resource A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available. genomics, genome, transcriptomics, protein-protein interaction, sequence typing, proteobacteria, brucella, rickettsia, coxiella, coronavirus, calicivirus, lyssavirus, virus, hepatitis a, hepatitis e, pathway, proteome, metabolic pathway, drug, vaccine, diagnostics, FASEB list is listed by: OMICtools
has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA
NIAID PMID:24225323
PMID:17142235
Free, Public, Acknowledgement requested r3d100010142, OMICS_01658, nlx_17476 http://patricbrc.vbi.vt.edu/portal/portal/patric/Home, https://doi.org/10.17616/R3WS3X http://patric.vbi.vt.edu/ SCR_004154 PathoSystems Resource Integration Center, PATRIC, Pathosystems Resource Integration Center 2026-07-30 09:27:01 1083
Gene Weaver
 
Resource Report
Resource Website
10+ mentions
Gene Weaver (RRID:SCR_003009) service resource, data repository, data analysis service, data or information resource, database, storage service resource, analysis service resource, production service resource Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration. phenotype, microarray, gene, genome, functional genomics, process, pathway, function, gene set, genomic data integration, analysis, visualization is used by: NIF Data Federation
is used by: Integrated Datasets
is listed by: OMICtools
is related to: Integrated Manually Extracted Annotation
has parent organization: Jackson Laboratory
Integrative Neuroscience Initiative on Alcoholism ;
NIAAA U01 AA13499;
NIAAA U24 AA13513;
NIAAA R01 AA18776
PMID:22080549
PMID:19733230
Free, Freely available r3d100012464, OMICS_02232, nif-0000-00517 http://ontologicaldiscovery.org/, https://doi.org/10.17616/R3248T SCR_003009 GeneWeaver, GeneWeaver - A system for the integration of functional genomics experiments, Ontological Discovery Environment, GeneWeaver.org 2026-07-30 09:26:46 34
VMD
 
Resource Report
Resource Website
1+ mentions
VMD (RRID:SCR_004905) PAMGO_VMD, VMD service resource, data analysis service, data or information resource, database, production service resource, analysis service resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Database covering a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at Virginia Bioinformatics Institute. The data comes from different sources and has genomes of 3 oomycetes pathogens: Phytophthora sojae, Phytophthora ramorum and Hyaloperonospora arabidopsidis. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. Two different statistical methods were used to validate these gene models, Fickett''''s and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum could be assigned. An easy-to-use genome browser was created to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs. microbial genome sequence, genome, genome sequence, genome model, gene, image, oomycete, fungus, bacteria, phytophthora sojae, phytophthora ramorum, hyaloperonospora arabidopsidis, plant is used by: NIF Data Federation
is related to: AmiGO
has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA
USDA Cooperative State Research Education and Extension Service 2002-35600-12747;
USDA Cooperative State Research Education and Extension Service 2004-35600-15055;
NSF MCB-0242131;
NSF EF-0412213;
NSF DBI-0211863
PMID:16381891 THIS RESOURCE IS NO LONGER IN SERVICE nlx_87328 http://phytophthora.vbi.vt.edu SCR_004905 VBI Microbial Database, Virginia Bioinformatics Institute Microbial Database 2026-07-30 09:27:04 8
Differential Methylation Analysis Package
 
Resource Report
Resource Website
Differential Methylation Analysis Package (RRID:SCR_019148) DMAP data processing software, software toolkit, data analysis software, software resource, software application Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity. Genomic DNA methylation, DNA methylation analysis, bisulphite sequenced data, reference methylomes generation, genome, aligned SAM files processing, differentially methylated regions has parent organization: University of Otago; Dunedin; New Zealand National Centre for Growth and Development and Health Research Council ;
New Zealand
PMID:24608764 Free, Freely available SCR_019148 2026-07-30 09:30:41 0
EnteroBase
 
Resource Report
Resource Website
100+ mentions
EnteroBase (RRID:SCR_019019) data access protocol, software resource, web service, data or information resource, database Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
has parent organization: University of Warwick; Coventry; United Kingdom
Biotechnology and Biological Sciences Research Council ;
Wellcome Trust
Restricted biotools:Enterobase https://bio.tools/EnteroBase SCR_019019 2026-07-30 09:30:30 233
Rickettsia Genome Database
 
Resource Report
Resource Website
1+ mentions
Rickettsia Genome Database (RRID:SCR_007102) data or information resource, database, image THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Rickettsia are obligate intracellular bacteria living in arthropods. They occasionally cause diseases in humans. To understand their pathogenicity, physiologies and evolutionary mechanisms, RicBase is sequencing different species of Rickettsia. Up to now we have determined the genome sequences of R. conorii, R. felis, R. bellii, R. africae, and R. massiliae. The RicBase aims to organize the genomic data to assist followup studies of Rickettsia. This website contains information on R. conorii and R. prowazekii. A R. conorii and R. prowazekii comparative genome map is also available. Images of genome maps, dendrogram, and sequence alignment allow users to gain a visualization of the diagrams. evolutionary, africae, alignment, arthropod, bacteria, bellii, conorii, dendrogram, disease, genome, genomic, human, intracellular, massiliae, mechanism, pathogenicity, physiology, prowazekii, rickettsia, sequence, specie, journal article, topical portal THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-20993 SCR_007102 RicBase 2026-07-30 09:27:36 1
Genomic HyperBrowser
 
Resource Report
Resource Website
10+ mentions
Genomic HyperBrowser (RRID:SCR_010909) Genomic HyperBrowser service resource, production service resource, analysis service resource, data analysis service 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 2026-07-30 09:28:39 20
UCSC Cancer Genomics Browser
 
Resource Report
Resource Website
500+ mentions
UCSC Cancer Genomics Browser (RRID:SCR_011796) Cancer Genomics Browser data or information resource, database, service resource A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets. genome, genomics, clinical, next-generation sequencing, chromosome, gene, FASEB list is listed by: OMICtools
has parent organization: University of California at Santa Cruz; California; USA
Cancer NCI ;
NHGRI ;
American Association for Cancer Research ;
UCSF Comprehensive Cancer Center ;
California Institute for Quantitative Biosciences
PMID:23109555
PMID:21059681
PMID:19333237
Acknowledgement requested OMICS_00925 SCR_011796 2026-07-30 09:28:38 530
miRanda
 
Resource Report
Resource Website
100+ mentions
miRanda (RRID:SCR_017496) data or information resource, database, service resource Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list is listed by: SoftCite NIGMS ;
Atlantic Philanthropies ;
Alfred W. Bressler Scholars Endowment Fund
PMID:18158296 THIS RESOURCE IS NO LONGER IN SERVICE http://www.microrna.org/microrna/home.do SCR_017496 MicroRNA.org. microrna.org 2026-07-30 09:30:11 210

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