Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ISCA Consortium Resource Report Resource Website 50+ mentions |
ISCA Consortium (RRID:SCR_006168) | ISCA Consortium, ISCA | community building portal, consortium, data or information resource, database, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 22, 2022. A rapidly growing group of clinical cytogenetics and molecular genetics laboratories committed to improving quality of patient care related to clinical genetic testing using new molecular cytogenetic technologies including array comparative genomic hybridization (aCGH) and quantitative SNP analysis by microarrays or bead chip technology. They improve clinical care by providing a large publicly available database and forum where clinicians and researchers can share knowledge to expedite the understanding of copy number variation (CNV) in an abnormal population. The ISCA database contains whole genome array data from a subset of the ISCA Consortium clinical diagnostic laboratories. Array analysis was carried out on individuals with phenotypes including intellectual disability, autism, and developmental delay. Efforts of the Consortium include: # Clinical Utility: The ISCA Consortium has made recommendations regarding the appropriate clinical indications for cytogenetic array testing (Miller et al. AJHG 2010, PMID: 20466091). Currently, discussions are focused on pediatric applications for children with unexplained developmental delay, intellectual disability, autism and other developmental disabilities. A separate committee has been developed to address appropriate cancer genetic applications (http://www.urmc.rochester.edu/ccmc/). # Evidence-based standards for cytogenomic array design: The Consortium will develop recommendations for standards for the design, resolution and content of cytogenomic arrays using an evidence-based process and an international panel of experts in clinical genetics, clinical laboratory genetics (cytogenetics and molecular genetics), genomics and bioinformatics. This design is intended to be platform and vendor-neutral (common denominator is genome sequence coordinates), and is a dynamic process with input from the broader genetics community and evidence-based review by the expert panel (which will evolve into a Standing Committee with international representation). # Public Database for clinical and research community: It is essential that publicly available databases be created and maintained for cytogenetic array data generated in clinical testing laboratories. The ISCA data will be held in dbGaP and dbVar at NCBI/NIH and curated by a committee of clinical genetics laboratory experts. The very high quality of copy number data (i.e., deletions and duplications) coming from clinical laboratories combined with expert curation will produce an invaluable resource to the clinical and research communities. # Standards for interpretation of cytogenetic array results: Using the ISCA Database, along with other genomic and genetics databases, the Consortium will develop recommendations for the interpretation and reporting of pathogenic vs. benign copy number changes as well as imbalances of unknown clinical significance. | clinical, cytogenetics, molecular genetics, genetic testing, molecular cytogenetic technology, array comparative genomic hybridization, quantitative snp analysis, microarray, bead chip, genome, array, phenotype, copy number, deletion, duplication, copy number variation, FASEB list |
is related to: Database of Genomic Variants Archive (DGVa) is related to: NCBI database of Genotypes and Phenotypes (dbGap) is related to: UCSC Genome Browser |
Intellectual disability, Developmental delay, Etc., Autism | This resource is no longer in service | nlx_151670 | SCR_006168 | ISCA Consortium and Public Database, International Standards for Cytogenomic Arrays (ISCA) Consortium, International Standards For Cytogenomic Arrays Consortium | 2026-09-12 01:00:11 | 78 | ||||||
|
Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data or information resource, data repository, database, service resource, storage service resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 | SCR_006307 | 2026-09-12 01:00:12 | 1104 | |||||
|
Candidate Genes to Inherited Diseases Resource Report Resource Website 1+ mentions |
Candidate Genes to Inherited Diseases (RRID:SCR_008190) | G2D | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases. | function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data set, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Molecular Biology Laboratory has parent organization: EMBL - Bork Group |
PMID:16115313 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21162, biotools:g2d | http://www.bork.embl-heidelberg.de/g2d/, http://www.ogic.ca/projects/g2d_2/, https://bio.tools/g2d | SCR_008190 | G2D - Candidate Genes to Inherited Diseases, Genes2Diseases | 2026-09-12 01:00:13 | 2 | |||||
|
AGI Resource Report Resource Website 10+ mentions |
AGI (RRID:SCR_007203) | AGI | data or information resource, disease-related portal, portal, research forum portal, topical portal | Their primary focus is in the area of structural, evolutionary and functional genomics of crop plants. AGI is divided into 5 Centers each lead by a Center Leader and a senior Manager (BAC Library Construction Center, BAC/EST Resource Center, Sequencing & Physical Mapping Center (including: production sequencing and fingerprinting, and sequence finishing), Bioinformatics Center and the Evolutionary and Functional Genomics Center). AGI is housed in the state of the art Thomas W. Keating Bioresearch Building on the northeast part of campus near the Medical School. AGI currently employees about 30 scientists and is primarily funded through federal grants, private contracts, and the Bud Antle Endowed Chair in Plant Molecular Genetics. Sponsors: AGI is supported by Bio5, Plant Sciences, National Science Foundation, National Institues oh Health, and USDA. | genomics, structural, evolutionary, functional, genome, crop, plant, bac, est, resource, physical, sequencing, fingerprinting, bioinformatics, evoluntionary | has parent organization: University of Arizona; Arizona; USA | nif-0000-30120 | SCR_007203 | Arizona Genomics Institute, The Arizona Genomics Institute | 2026-09-12 01:00:13 | 18 | ||||||||
|
Frey Lab Resource Report Resource Website 1+ mentions |
Frey Lab (RRID:SCR_008859) | Frey Lab | data or information resource, laboratory portal, organization portal, portal, topical portal | The Frey Lab develops techniques that use large scale datasets to derive predictive models of how genes and many other genomic features act in combination to produce genetic messages that control cellular activities. We have most recently focused on how organisms use alternative splicing to generate a tremendous level of biological complexity that cannot be explained by gene expression alone (Nature, 2010). Some of the tools, software and databases provided by the Frey Lab are affinity propagation, splicing prediction, PTMClust - A Post-translational Modification Refinement Algorithm, the ''epitome'': A new model of patterns, transformation invariant clustering and subspaces, learning flexible sprites from images and videos, phase unwrapping by loopy belief propagation, useful Matlab scripts, bioinformatics links, and SeedSearcher: A motif finder. | gene, genetic message, affinity propagation, alternative splicing prediction, motif, tool, software, database, flobject analysis, signal processing, graphical model, inference algorithm, computational vision, alternative splicing, transcriptome, genome, gene function prediction, gene function, computational biology, message passing | has parent organization: University of Toronto; Ontario; Canada | nlx_149187 | SCR_008859 | U of T Frey Lab, University of Toronto - Frey Lab, Frey Lab - Probabilistic and Statistical Inference Group University of Toronto | 2026-09-12 01:00:14 | 1 | ||||||||
|
LINKDATAGEN Resource Report Resource Website 1+ mentions |
LINKDATAGEN (RRID:SCR_015625) | data analysis software, data processing software, sequence analysis software, software application, software resource | Perl tool that generates linkage mapping input files using data from HAPMAP Phase III populations. It provides rudimentary error checks and is easily amended for personal linkage mapping preferences. | annotation, snp, sequencing, genome, linkage, mapping, perl, hapmap phase iii | has parent organization: Walter and Eliza Hall Institute of Medical Research; Victoria; Australia | NHMRC 461269; NHMRC 490037; NHMRC 406657 |
PMID:19435744 PMID:21917141 |
Free, Available for download | SCR_015625 | 2026-09-12 01:00:17 | 7 | ||||||||
|
GWASrap Resource Report Resource Website 1+ mentions |
GWASrap (RRID:SCR_013144) | GWASrap | analysis service resource, data access protocol, data analysis service, data or information resource, data set, production service resource, service resource, software resource, web service | GWASrap is a comprehensive web-based bioinformatics tool to systematically support variant representation, annotation and prioritization for data generated from genome-wide association studies (GWAS) and Next Generation Sequencing (NGS). Our web-based framework utilizes state-of-the-art web technologies to maximize user interaction and visualization of the results. For a given SNP dataset with its P-values, GWASrap will first provide a Circos-style plot to visualize any genetic variants at either the genome or chromosome level. The tool then combines different genomic features (SNP/CNV density, disease susceptibility loci, etc.) with comprehensive annotations that give the researcher an intuitive view of the functional significance of the different genomic regions. The detailed statistics of the underlying study are also displayed on the web page, including variant distribution in different functional categories, classic Manhattan plot and QQ plot. Users can perform interactive operations in the Manhattan panel, such as zooming in and out to search regions or markers of interest. The system can also display a comprehensive range of relevant information from variant genetic attributes to nearby genomic elements, such as enhancers or non-coding RNAs. Furthermore, researchers can obtain extensive functional predictions for various features including transcription factor-binding sites, miRNA and miRNA target sites, and their predicted changes caused by the genetic variants. Our system can re-prioritize genetic variants by combining the original statistical value and variant prioritization score based on a simple additive effect equation. Researchers can also re-evaluate the significance of a trait/disease-associated SNP (TAS) using the dynamic linkage disequilibrium (LD) panel or the tree-like network panel. The GWASrap supports input variants in different formats, not only common variants with a dbSNP rs ID but also rare variants from NGS data, which are represented by chromosome and locations. GWASrap provides a range of web services for data retrieving about the annotation information and effect prediction of each variant in dbSNP using the SOAP interface. The WSDL for each service is available in the API tab. Each service returns JSON string including all related information with key/value. GWASrap provides running results about some current published GWAS as well as a category view for each hot disease / trait. The dataset is brought from published database GWAS or curated from literature. | genome wide association study, annotation, next generation sequencing, genetic variant, prioritize, visualize, genome, chromosome, functional prediction, transcription factor-binding site, mirna, mirna target site, prediction, target site, transcription factor, binding site, statistics, trait/disease-associated snp, single nucleotide polymorphism, trait, disease, representation, linkage disequilibrium | is related to: GWASdb | Bipolar Disorder, Alzheimer's disease, Depression, Parkinson Disease, Diabetes Mellitus, Amyotrophic Lateral Sclerosis, Rheumatoid Arthritis, HIV-1 Disease, Human immunodeficiency virus, Hematopoietic System Disease, Prostate Cancer, Coronary Artery Disease, Schizophrenia, Arteriopathy, Multiple Sclerosis, Crohn''''s Disease, Hypertension, Breast Cancer | PMID:22801476 | nlx_151497 | SCR_013144 | GWASrap - SNPs Representing Annotating and Prioritizing Tool for Genome Wide Association Study | 2026-09-12 01:00:16 | 2 | ||||||
|
Pilon Resource Report Resource Website 1000+ mentions |
Pilon (RRID:SCR_014731) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome. | automatically, improve, draft, assembly, variation, strain, genome, read, alignment, analysis, inconsistency, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: shovill is hosted by: GitHub |
DOI:10.1371/journal.pone.0112963 DOI:10.1371/journal.pone.0112963 |
Available for download, Acknowledgement requested | OMICS_14553, biotools:pilon | https://github.com/broadinstitute/pilon/wiki, https://bio.tools/pilon, https://sources.debian.org/src/pilon/ | SCR_014731 | 2026-09-12 01:00:17 | 3377 | |||||||
|
Hinge Resource Report Resource Website 1+ mentions |
Hinge (RRID:SCR_016135) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution. | long, read, genome, assembly, hinging, sequence, optimal, repeat, resolution |
is listed by: Debian is listed by: OMICtools |
PMID:28320918 | Free, Available for download | OMICS_12339 | https://sources.debian.org/src/hinge/ | SCR_016135 | 2026-09-12 01:00:18 | 9 | |||||||
|
OGDraw Resource Report Resource Website 100+ mentions |
OGDraw (RRID:SCR_017337) | OGDRAW | data processing software, data visualization software, service resource, software application, software resource, software toolkit | Software package for graphical visualization of organellar genomes. Converts annotations in GenBank format into graphical maps. Used to create visual representations of circular and linear annotated genome sequences provided as GenBank files or accession numbers. | graphical, visualization, organellar, genome, convert, annotation, GenBank, format, map, DNA, sequence | works with: GenBank | Max Planck Society | PMID:30949694 | Free, Freely available | SCR_017337 | Draw Organelle Genome Maps, OrganellarGenomeDRAW | 2026-09-12 01:00:20 | 359 | ||||||
|
ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. | comparative, analysis, sequence, bacteria, genome, reconstruct, recombination, events, ancestry, bayesian |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882; Wellcome Trust WT082930MA |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-09-12 01:00:18 | 8 | ||||||
|
Optimus Pipeline Resource Report Resource Website 1+ mentions |
Optimus Pipeline (RRID:SCR_018908) | data analysis software, data processing software, software application, software resource | Optimus is a pipeline developed by the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA) Project that supports processing of any 3' single-cell and single-nuclei expression data generated with the 10x Genomic v2 or v3 assay. It is an alignment and transcriptome quantification pipeline that corrects cell barcodes, aligns reads to the genome, corrects Unique Molecular Identifiers (UMIs), generates an expression matrix in a UMI-aware manner, calculates summary metrics for genes and cells, detects empty droplets, returns read outputs in BAM format, and returns gene counts in NumPy matrix and Loom matrix formats. | Data, single cell data, 10x technology data, cell bar code correction pipeline, reads alignment, genome, unique molecular identifier correction, mouse data sets analysis, human data sets analysis, |
is used by: BICCN is related to: Human Cell Atlas |
Free, Available for download, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/optimus | SCR_018908 | Optimus | 2026-09-12 01:00:21 | 2 | ||||||||
|
CAZy- Carbohydrate Active Enzyme Resource Report Resource Website 1000+ mentions |
CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) | CAZy | data or information resource, database | Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site. | carbohydrate, carbohydrate-binding, carbohydrate binding module, carbohydrate esterase, catalytic binding, glycosidic bond, glycosidic hydrolase, glycosyl transferase, polysaccharide lyase, enzyme class, enzyme, module, genome, virus, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Aix-Marseille University; Provence-Alpes-Cote d'Azur; France |
PMID:24270786 | r3d100012321, biotools:cazy, OMICS_01677, nif-0000-02642, SCR_012935 | https://bio.tools/cazy | SCR_012909 | Carbohydrate-Active enZYme, Carbohydrate-Active enZYmes Database | 2026-09-12 01:00:36 | 2435 | ||||||
|
MUMmer Resource Report Resource Website 500+ mentions |
MUMmer (RRID:SCR_018171) | alignment software, data processing software, image analysis software, software application, software resource | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NIAID N01 AI15447; NLM R01 LM06845; NSF IIS 9902923 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer, https://bio.tools/mummer, https://sources.debian.org/src/mummer/ | SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-09-12 12:58:58 | 547 | |||||
|
Global Initiative on Sharing All Influenza Data Resource Report Resource Website 1000+ mentions |
Global Initiative on Sharing All Influenza Data (RRID:SCR_018251) | GISAID | data or information resource, database, disease-related portal, portal, topical portal | Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data. | hCoV19, hCoV-19 genome sequence, data, coronavirus, SARS coronavirus, Coronavirus, genome, genome database, influenza, SARS-CoV infection, SARS-CoV-2, COVID-19 |
lists: Health Data Research UK COVID-19 Initiative is listed by: Data and Computational Resources to Address COVID-19 is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation works with: Nextstrain |
CoV19, COVID19, COVID-19 | PMID:28382917 | Restricted | SCR_018279, r3d100010126, SCR_018318 | https://doi.org/10.17616/R3Q59F | SCR_018251 | 2026-09-12 12:58:59 | 2596 | |||||
|
SARS-CoV-2-Sequences Resource Report Resource Website 10+ mentions |
SARS-CoV-2-Sequences (RRID:SCR_018319) | data or information resource, data repository, data set, service resource, storage service resource | Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released. | SARS-CoV-2, SARS coronavirus, SARS-CoV infection, Coronavirus, data, SARS-CoV-2 sequence collection, nucleotide, genome, Betacoronavirus, protein |
works with: GenBank works with: NCBI Sequence Read Archive (SRA) |
COVID-19 | The Federal Government | Free, Available for download, Freely available | SCR_018319 | Severe Acute Respiratory Syndrome CoronaVirus 2 Sequences | 2026-09-12 12:58:59 | 37 | |||||||
|
CRISPR-ERA Resource Report Resource Website 10+ mentions |
CRISPR-ERA (RRID:SCR_018710) | data access protocol, service resource, software resource, web service | Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design. | Design tool, CRISPR mediated gene editing, gene repression, gene activation, guide RNA design, genome, automated genome, sgRNA design, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
FANEDD ; NIDA R01 DA036858; NIDCR ; NIH Office of The Director ; NIH Office of the Director OD017887; NSFC |
PMID:26209430 | Free, Freely available | biotools:CRISPR-ERA | https://bio.tools/CRISPR-ERA | SCR_018710 | CRISP-Editing, Repression and Activation | 2026-09-12 12:59:05 | 13 | |||||
|
BeetleBase Resource Report Resource Website 50+ mentions |
BeetleBase (RRID:SCR_001955) | BEETLEBASE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded. | red flour beetle, tribolium castaneum, sequence data, gene, mutant, genetic marker, expressed sequence tag, genome, blast, model organism, insect, developmental biology, genomics, genetics, entomology, development, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: RefSeq has parent organization: Kansas State University; Kansas; USA |
NCRR P20 RR16475 | PMID:18362917 PMID:17090595 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02599, biotools:beetlebase, r3d100010921 | https://bio.tools/beetlebase, https://doi.org/10.17616/R3G61K | http://bioinformatics.k-state.edu/BeetleBase/, http://www.bioinformatics.ksu.edu/BeetleBase/ | SCR_001955 | 2026-09-12 01:00:07 | 82 | ||||
|
University of Bergen Computational Biology Unit Resource Report Resource Website 1+ mentions |
University of Bergen Computational Biology Unit (RRID:SCR_002970) | UiB CBU | data or information resource, department portal, organization portal, portal | An inter-department center that conducts bioinformatics research and expands the interface between bioinformatics and experimental biological and biomedical research. The unit is closely associated with the the Bioinformatics group at the Department of Informatics (II) and has tight links with the Sars Centre for Marine Molecular biology (SARS) and the Department of Molecular Biology (MBI). Six research groups are currently associated with CBU with projects that include sequence and structure analysis, molecular evolution, genome annotation and genomics data analysis. CBU also provides services and contributes to bioinformatics education primarily through training courses. | computational, biology, bioinformatics, analysis, structure, molecular, evolution, genome, annotation, functional genomic, programming, rna, dna, molecular biology, protein modelling, integrated genomics, evolutionary genomics | has parent organization: University of Bergen; Bergen; Norway | Research Council of Norway ; FUGE programme |
nif-0000-30147 | http://www.cbu.uib.no | SCR_002970 | UiB Computational Biology Unit | 2026-09-12 01:00:09 | 1 | ||||||
|
COnsensus-DEgenerate Hybride Oligonucleotide Primers Resource Report Resource Website 1+ mentions |
COnsensus-DEgenerate Hybride Oligonucleotide Primers (RRID:SCR_002875) | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | fractionation, gel, 3', amplification, clone, dna, genome, homolog, human, hybrid, molecule, oligonucleotide, pcr, plant, primer, protein, sequence, transcriptase-methyltransferase |
is related to: OMICtools has parent organization: University of Washington; Seattle; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25557 | SCR_002875 | CODEHOP | 2026-09-12 01:00:09 | 8 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
