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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Nucleotide database Resource Report Resource Website 100+ mentions |
Nucleotide database (RRID:SCR_004630) | nucest | data repository, database, storage service resource, service resource, data or information resource | Nucleotide database as collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. | Genome, gene, transcript sequence data, GenBank, RefSeq, TPA, PDB, gold standard |
is listed by: re3data.org is related to: BMAP cDNA Resources is related to: GenBank has parent organization: NCBI |
PMID:8401577 | Free, Freely available | SCR_016578, nlx_62971 | SCR_004630 | 2026-02-16 09:46:23 | 167 | |||||||
|
PANTHER Resource Report Resource Website 5000+ mentions |
PANTHER (RRID:SCR_004869) | PANTHER | controlled vocabulary, data analysis service, analysis service resource, ontology, database, production service resource, service resource, data or information resource | System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | hidden markov model, human, mouse, genome, protein, gene, function, pathway, ortholog, phylogenetic tree, gene ortholog, protein family, gene function, evolution, data set, molecular function, biological process, cellular component, transcript, FASEB list |
is used by: NIF Data Federation is used by: YPED is used by: EMBRYS is related to: Gene Ontology is related to: Pathway Commons is related to: KOBAS has parent organization: University of Southern California; Los Angeles; USA is parent organization of: PANTHER Evolutionary analysis of coding SNPs |
NIGMS GM081084 | PMID:23193289 PMID:20015972 PMID:12952881 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015893, nlx_84521 | SCR_004869 | PANTHER Classification System, Protein ANalysis THrough Evolutionary Relationships Classification System, Protein ANalysis THrough Evolutionary Relationships, PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System | 2026-02-16 09:46:23 | 8331 | |||||
|
Eurexpress Resource Report Resource Website 1+ mentions |
Eurexpress (RRID:SCR_005093) | Eurexpress | atlas, image collection, expression atlas, database, data or information resource | Genome transcriptome atlas by RNA in situ hybridization on sagittal sections of developing mouse at embryonic day 14.5. Consists of searchable database of annotated images that can be interactively viewed. Anatomy based expression profiles for coding genes and microRNAs, tissue specific genes. Expression data generated by using human and murine tissue arrays. | Genome, transcriptome, atlas, RNA, in situ, hybrydization, sagittal, section, developing, mouse, embryo, expression, gene |
is listed by: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) is related to: EMAGE Gene Expression Database is related to: aGEM has parent organization: Telethon Institute of Genetics and Medicine; Naples; Italy |
European Union ; VI Framework ; Telethon Foundation ; Swiss National Science Foundation ; Max Planck Society ; MRC ; Association pour la Recherche sur le Cancer ; Ingenio 2010 MEuropean Union |
PMID:21267068 | nif-0000-00243 | http://www.eurexpress.org/ee/databases/anatomy/treeFrames.jsp, http://www.eurexpress.org/ee/ | SCR_005093 | Eurexpress atlas, Transcriptome Atlas Database for Mouse Embryo | 2026-02-16 09:46:23 | 3 | |||||
|
SMART Resource Report Resource Website 5000+ mentions |
SMART (RRID:SCR_005026) | SMART | web service, data analysis service, analysis service resource, data access protocol, database, software resource, production service resource, service resource, data or information resource | Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures. | extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiary, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: bio.tools is listed by: Debian is related to: Eukaryotic Linear Motif is related to: Conserved Domain Database is related to: GOTaxExplorer has parent organization: EMBL - Bork Group |
European Union | PMID:18978020 PMID:16381859 PMID:14681379 PMID:10592234 PMID:9847187 PMID:9600884 |
Free, Freely available | nif-0000-03471, biotools:smart | http://smart.embl-heidelberg.de/ https://bio.tools/smart |
SCR_005026 | Simple Modular Architecture Research Tool | 2026-02-16 09:46:26 | 6760 | ||||
|
Database of Genomic Variants Archive (DGVa) Resource Report Resource Website 100+ mentions |
Database of Genomic Variants Archive (DGVa) (RRID:SCR_004896) | DGVa | data repository, database, storage service resource, service resource, data or information resource | Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA). | genome, dna, gene, expression, genetics, mapping, structural, variant, gold standard |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is related to: dbVar is related to: ISCA Consortium is related to: Database of Genomic Variants is related to: Ensembl Variation has parent organization: European Bioinformatics Institute |
PMID:23193291 PMID:24174537 |
Free, Freely available | nlx_86626, r3d100010814 | https://doi.org/10.17616/R3HK7Z | http://www.ebi.ac.uk/dgva/page.php, http://www.ebi.ac.uk/dgva/ | SCR_004896 | , DGVarchive, DGVa, Database of Genomic Variants Archive | 2026-02-16 09:46:32 | 145 | ||||
|
PHAge Search Tool Resource Report Resource Website 100+ mentions |
PHAge Search Tool (RRID:SCR_005184) | PHAST | data set, data analysis service, analysis service resource, production service resource, service resource, data or information resource | A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available. | prophage sequence, genome, prophage, sequence, bacterial genome, plasmid, dna sequence, graph, phage, annotate, virus, nucleotide sequence, fasta, annotated genome, genbank, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Alberta; Alberta; Canada |
PMID:21672955 | Acknowledgement requested | biotools:phast, OMICS_00180 | https://bio.tools/phast | SCR_005184 | PHAST - PHAge Search Tool | 2026-02-16 09:46:26 | 225 | |||||
|
DBD: Transcription factor prediction database Resource Report Resource Website 10+ mentions |
DBD: Transcription factor prediction database (RRID:SCR_002300) | DBD | service resource, data or information resource, database | Database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries. Benchmarks of the transcription factor predictions show they are accurate and have wide coverage on a genomic scale. The DBD consists of predicted transcription factor repertoires for 930 completely sequenced genomes. | predicted transcription factor, transcription factor, dna-binding domain, proteome, sequence, domain family, protein sequence, genome, prediction |
is listed by: OMICtools is related to: SUPERFAMILY is related to: Pfam has parent organization: MRC Laboratory of Molecular Biology |
PMID:18073188 PMID:16381970 |
Acknowledgement requested | nif-0000-02726, OMICS_00531 | SCR_002300 | DNA-binding domain | 2026-02-16 09:45:43 | 10 | ||||||
|
SSCprofiler Resource Report Resource Website 1+ mentions |
SSCprofiler (RRID:SCR_001282) | SSCprofiler | production service resource, service resource, data analysis service, analysis service resource | Tool which can be used to identify novel miRNA gene candidates in the human genome. | microrna, gene, genome, sequence, structure, conservation |
is listed by: OMICtools has parent organization: Institute of Molecular Biology and Biotechnology; Heraklion; Greece |
PMID:19324892 | Free, Freely available | OMICS_02055 | SCR_001282 | Sequence Structure and Conservation profiler | 2026-02-16 09:45:27 | 3 | ||||||
|
HiPipe Resource Report Resource Website 1+ mentions |
HiPipe (RRID:SCR_001215) | HiPipe | production service resource, service resource, data analysis service, analysis service resource | Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task. | next-generation sequencing, dna, rna, differential expression, mirna, gene fusion, variant, genome, exome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Academia Sinica; Taipei; Taiwan |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02128, biotools:hipipe | https://bio.tools/hipipe | SCR_001215 | HiPipe - High Performance Pipelines for NGS Data Analysis | 2026-02-16 09:45:26 | 2 | ||||||
|
WTCHG Genome Scan Viewer Resource Report Resource Website 1+ mentions |
WTCHG Genome Scan Viewer (RRID:SCR_001635) | GSCANDB | service resource, data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database / display tool of genome scans, with a web interface that lets the user view the data. It does not perform any analyses - these must be done by other software, and the results uploaded into it. The basic features of GSCANDB are: * Parallel viewing of scans for multiple phenotypes. * Parallel analyses of the same scan data. * Genome-wide views of genome scans * Chromosomal region views, with zooming * Gene and SNP Annotation is shown at high zoom levels * Haplotype block structure viewing * The positions of known Trait Loci can be overlayed and queried. * Links to Ensembl, MGI, NCBI, UCSC and other genome data browsers. In GSCANDB, a genome scan has a wide definition, including not only the usual statistical genetic measures of association between genetic variation at a series of loci and variation in a phenotype, but any quantitative measure that varies along the genome. This includes for example competitive genome hybridization data and some kinds of gene expression measurements. | genome, gene, snp, trait, genotype, phenotype, visualization, region, chromosome, quantitative trait locus, hybridization, gene expression | has parent organization: University of Oxford; Oxford; United Kingdom | NIAAA U01AA014425; NCRR R24RR015116; NIGMS R01GM072863; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153902 | SCR_001635 | Wellcome Trust Centre for Human Genetics Genome Scan Viewer, Genome Scan Viewer, Genome Scan Database | 2026-02-16 09:45:32 | 3 | ||||||
|
HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | service resource, data or information resource, database | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene https://doi.org/10.17616/R3889F |
SCR_002924 | NCBI HomoloGene | 2026-02-16 09:45:55 | 437 | |||||
|
BiSearch: Primer Design and Search Tool Resource Report Resource Website 50+ mentions |
BiSearch: Primer Design and Search Tool (RRID:SCR_002980) | BiSearch | production service resource, service resource, data analysis service, analysis service resource | BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method. This is especially recommended when primers are designed to amplify the highly redundant bisulfite treated sequences. It has the unique property of analyzing the primer pairs for mispriming sites on the bisulfite-treated genome and determines potential non-specific amplification products with a new search algorithm. The options of primer-design and analysis for mispriming sites can be used sequentially or separately, both on bisulfite-treated and untreated sequences. In silico and in vitro tests of the software suggest that new PCR strategies may increase the efficiency of the amplification. | dna, sequence, primer, design, algorithm, analysis, priming, bisulfite, genome, amplification, in vitro, in silico, amplification, epcr, cytosines | has parent organization: Hungarian Academy of Sciences; Budapest; Hungary | PXE International Inc. GVOP-3.1.1-2004-05-0143/3.0; Boolyai Janos Scholarship ; OTKA T34131; OTKA D42207 |
PMID:17022803 PMID:15653630 |
nif-0000-30170 | SCR_002980 | 2026-02-16 09:45:53 | 50 | |||||||
|
JCVI GenProp Resource Report Resource Website 1+ mentions |
JCVI GenProp (RRID:SCR_004592) | JCVI GenProp | service resource, data or information resource, database | The Genome Properties system consists of a suite of Properties which are carefully defined attributes of prokaryotic organisms whose status can be described by numerical values or controlled vocabulary terms for individual completely sequenced genomes. The system has been designed to capture the widest possible range of attributes and currently encompasses taxonomic terms, genometric calculations, metabolic pathways, systems of interacting macromolecular components and quantitative and descriptive experimental observations (phenotypes) from the literature. You may search the Genome Properties Database in 1 of 3 ways: * Search For Predicted Properties in the CMR: The Genome Property Search allows you to search the Genome Property database for state information for selected genomes and properties. * Perform a Keyword Search for a Specific Property: Lists all Genome Properties that match a specific text string. You can choose to search All Fields within a genome property or the Property Name. * Browse Top Level Genome Properties: Click on the properties to see the specific genome property report page. The Genome Properties system presents key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties. | prokaryote, genome, genomics, a | has parent organization: JCVI CMR | NSF DBI-0110270; DOE DE-FG02-01ER63203 |
PMID:15347579 | nlx_58176 | http://www.tigr.org/Genome_Properties | SCR_004592 | Genome Properties, Genome Properties Database, JCVI CMR Genome Properties | 2026-02-16 09:46:23 | 1 | |||||
|
AVIA Resource Report Resource Website 1+ mentions |
AVIA (RRID:SCR_005172) | AVIA | production service resource, service resource, data analysis service, analysis service resource | An interactive web-based tool to explore and interpret large sets of genomic variations (single nucleotide variations and insertion/deletions) to help guide and summarize genomic experiments. The tool is based on coupling a comprehensive annotation pipeline with a flexible visualization method. They leveraged the ANNOVAR (Wang et. al, 2010) framework for assigning functional impact to genomic variations by extending its list of reference annotation databases (RefSeq, UCSC, SIFT, Polyphen etc.) with additional in-house developed sources (Non-B DB, PolyBrowse). Further, because many users also have their own annotation sources, they have added the ability to supply their own files as well. The results can be obtained in tabular format or as tracks in whole genome circular views generated by the Circos application (Krzywinski et. al, 2009). Users can also select different sets of pre-computed tracks, including whole genome distributions of different genomic features (genes, exons, repeats), as well as variations analysis tracks for the 69 CGI public genomes for reference. | genomic variation, single nucleotide variation, insertion, deletion, indel, genome, annotation, visualization, impact analysis, mirna snp, mirna, snp, subtractive analysis, protein coding |
is listed by: OMICtools has parent organization: Frederick National Laboratory for Cancer Research has parent organization: NCI-Frederick |
PMID:24215028 | Acknowledgement requested | OMICS_00168 | SCR_005172 | Annotation Visualization and Impact Analysis | 2026-02-16 09:46:26 | 9 | ||||||
|
NBC Resource Report Resource Website 1+ mentions |
NBC (RRID:SCR_004772) | NBC | production service resource, service resource, data analysis service, analysis service resource | Webserver for taxonomic classification of metagenomic reads. | metagenome, genome, virus, taxonomy, next-generation sequencing, taxonomic classification, classification |
is listed by: OMICtools has parent organization: Drexel University; Pennsylvania; USA |
NSF DBI-0845827; DOE DE-SC0004335 |
PMID:1062764 PMID:19956701 |
OMICS_01458 | SCR_004772 | Naive Bayes Classification tool, Na����ve Bayesian Classification tool, Naive Bayesian Classification Tool | 2026-02-16 09:46:30 | 3 | ||||||
|
Oncotator Resource Report Resource Website 100+ mentions |
Oncotator (RRID:SCR_005183) | Oncotator | production service resource, service resource, data analysis service, analysis service resource | A tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. Genomic Annotations, Protein Annotations, and Cancer Annotations are aggregated from many resources. A standalone version of Oncotator is being developed. | annotate, genomic, point mutation, indel, mutation, genome, protein, variant |
is listed by: OMICtools has parent organization: Broad Institute |
Cancer | OMICS_00178 | SCR_005183 | 2026-02-16 09:46:26 | 215 | ||||||||
|
BeetleBase Resource Report Resource Website 50+ mentions |
BeetleBase (RRID:SCR_001955) | BEETLEBASE | data analysis service, analysis service resource, database, production service resource, service resource, data or information 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 | 2026-02-16 09:45:41 | 82 | ||||
|
MycoCosm Resource Report Resource Website 100+ mentions |
MycoCosm (RRID:SCR_005312) | MycoCosm | data analysis service, analysis service resource, data repository, database, storage service resource, production service resource, service resource, data or information resource | Fungal genomics database and interactive analytical tools that integrates all fungal genomes for diverse fungi that are important for energy and environment, the focus of the JGI Fungal program. It integrates genomics data from the DOE JGI and its users and promotes user community participation in data submission, annotation and analysis. Over 100 newly sequenced and annotated fungal genomes from JGI and elsewhere are available to the public through MycoCosm, and new annotated genomes are being added to this resource upon completion of annotation. MycoCosm offers web-based genome analysis tools for fungal biologists to ''navigate'' through sequenced genomes and explore them in the context of ''genome-centric'' and ''comparative views''. | gene, genome, geneome map, jgi, fungus, genomics, energy, environment, annotation, FASEB list |
is listed by: OMICtools is related to: 1000 Fungal Genome Project has parent organization: DOE Joint Genome Institute |
DOE | PMID:24297253 PMID:22110030 |
Public, Acknowledgement requested, The community can contribute to this resource | OMICS_01657, nlx_144366, r3d100011751 | https://doi.org/10.17616/R3QQ0J | http://jgi.doe.gov/fungi | SCR_005312 | MycoCosm - the fungal genomics resource | 2026-02-16 09:46:39 | 240 | |||
|
University of Bergen Computational Biology Unit Resource Report Resource Website |
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 | 2026-02-16 09:45:55 | 0 | ||||||
|
COnsensus-DEgenerate Hybride Oligonucleotide Primers Resource Report Resource Website 1+ mentions |
COnsensus-DEgenerate Hybride Oligonucleotide Primers (RRID:SCR_002875) | software application, data processing software, data analysis software, data analysis service, analysis service resource, software resource, production service resource, service 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 | 2026-02-16 09:45:56 | 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.
