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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
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
TFSEARCH: Searching Transcription Factor Binding Sites
 
Resource Report
Resource Website
100+ mentions
TFSEARCH: Searching Transcription Factor Binding Sites (RRID:SCR_004262) production service resource, service resource, data analysis service, analysis service resource The TFSEARCH searches highly correlated sequence fragments against TFMATRIX transcription factor binding site profile database in the "TRANSFAC" databases developed at GBF-Braunschweig, Germany. The TFSEARCH program was written by Yutaka Akiyama (Kyoto University, currently at RWCP) in 1995. vertebrate, arthropod, plant, yeast, dna, sequence, FASEB list is related to: TFFACTOR
has parent organization: Computational Biology Research Center Core Facility
PMID:9399875 nlx_27602 http://www.cbrc.jp/research/db/TFSEARCH.html SCR_004262 TFSEARCH: DNA Transcription Factor Binding Site Prediction, Transcriptional Factor Search, TFSEARCH 2026-02-16 09:46:19 214
Mammalian Gene Collection
 
Resource Report
Resource Website
10+ mentions
Mammalian Gene Collection (RRID:SCR_007024) MGC material resource, biomaterial supply resource, cell repository NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). cell line, cdna, frozen, clone, vector, gene, open reading frame, sequence, expressed sequence tag, bio.tools, FASEB list is listed by: One Mind Biospecimen Bank Listing
is listed by: bio.tools
is listed by: Debian
is related to: One Mind Biospecimen Bank Listing
is related to: NIDDK Information Network (dkNET)
is related to: ATCC
is related to: GenBank
is related to: Invitrogen Clones
is related to: Open Biosystems
is related to: Zebrafish Gene Collection
has parent organization: National Cancer Institute
NIH Blueprint for Neuroscience Research Free, Freely available biotools:mammalian_gene_collection, nif-0000-00195 https://bio.tools/mammalian_gene_collection SCR_007024 Mammalian Gene Collection 2026-02-16 09:46:52 46
BioRep
 
Resource Report
Resource Website
100+ mentions
BioRep (RRID:SCR_004907) BioRep material resource, biomaterial supply resource, cell repository Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories. chromosome analysis, dhplc analysis, methylation, genotyping, gender analysis, sequencing service, nucleic acid isolation, catalog, cell line, dna, cell, tissue, frozen, liquid nitrogen, vapor nitrogen, refrigerator, fixed, paraffin embedded, slide, cryogenic, paraffin block, cryopreserved, molecular biology, microbiology, cytogenetics, media preparation, tissue microarray, cell array, frozen array, cell biology, research, transplantation, custom, blood, tissue, ebv transformed lymphoblast culture, fibroblast cell culture, nucleic acid, sequence, mycoplasma, karyotype is listed by: One Mind Biospecimen Bank Listing
is related to: Coriell Institute for Medical Research
Public: offer biorepository services to public and private research institutes, To the highest standards of quality and safety. BioRep is one of the few ''''Global Biorepository'''' able to serve the pharmaceutical industries for world wide clinical trials. nlx_87504 http://www.biorep.it/eng/ SCR_004907 2026-02-16 09:46:23 166
Washington University Basic Local Alignment Search Tool
 
Resource Report
Resource Website
1000+ mentions
Washington University Basic Local Alignment Search Tool (RRID:SCR_008285) data processing software, software application, software resource It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterized genes. evolutionary, fragment, function, functional, gene, genetic code, algorithm, align, alignment, blast, local, novel, nucleotide, pair, protein, region, segment, sensitivity, sequence, similarity, structure, tool has parent organization: European Molecular Biology Laboratory nif-0000-23905 SCR_008285 WU-BLAST2 2026-02-16 09:47:09 3631
CESG
 
Resource Report
Resource Website
1+ mentions
CESG (RRID:SCR_008451) CESG data or information resource, organization portal, portal It is a specialized research center supported by the Protein Structure Initiative (PSI) of the National Institute of General Medical Sciences (NIGMS), one of the National Institutes of Health (NIH). PSI is a federal, university, and industry effort aimed at dramatically reducing the costs and lessening the time it takes to determine a three-dimensional protein structure. The long-range goal of PSI is to solve 10,000 protein structures in 10 years and to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences. CESG is located within the Department of Biochemistry at the University of Wisconsin-Madison (Madison, WI) and the Department of Biochemistry at the Medical College of Wisconsin (Milwaukee, WI). CESG develops new methods and technologies to address unique eukaryotic bottlenecks and disseminates its methodologies and experimental results to the scientific community worldwide through: :- Cell-Free Protein Production Workshops :- Plasmids at PSI Materials Repository :- Posters Presented at Scientific Meetings :- Publications in PubMed / PubMed Central :- Sesame (LIMS) Available for Researchers :- Solved Structures in the Protein Data Bank :- Technology Dissemination Reports They have welcomed requests by researchers to solve eukaryotic protein structures, particularly medically relevant proteins, through our Online Structure Request System for Researchers. They have solved many community-nominated targets and deposited information about these targets in public databases and published on our investigations and findings. Sponsors: CESG is supported by NIH / NIGMS Protein Structure Initiative grant numbers U54 GM074901 and P50 GM064598. eukaryotic, structural, genomics, research, center, protein, structure, medical, science, health, atom, dna, sequence, knowledge, biochemistry, technology, cell, plasmid has parent organization: University of Wisconsin-Madison; Wisconsin; USA nif-0000-30322 SCR_008451 Center for Eukaryotic Structural Genomics, The Center for Eukaryotic Structural Genomics 2026-02-16 09:47:11 9
Center for Computational Biology at JHU
 
Resource Report
Resource Website
1+ mentions
Center for Computational Biology at JHU (RRID:SCR_016680) CCB at JHU data or information resource, organization portal, portal Center for Computational Biology as a joint research center in the McKusick-Nathans Institute of Genetic Medicine, spanning the School of Medicine, the Whiting School of Engineering, the Bloomberg School of Public Health, and the Krieger School of Arts & Sciences. Multidisciplinary center dedicated to research on genomics, genetics, DNA sequencing technology, and computational methods for DNA and RNA sequence analysis. center, computational, biology, genomics, genetics, DNA, RNA, sequence, technology, analysis has parent organization: Johns Hopkins University; Maryland; USA
is parent organization of: Centrifuge Classifier
SCR_016680 CCB at Johns Hopkins University, CCB at JHU, Center for Computational Biology at JHU, Center for Computational Biology at Johns Hopkins University 2026-02-16 09:49:05 1
GENCODE
 
Resource Report
Resource Website
5000+ mentions
Rating or validation data
GENCODE (RRID:SCR_014966) data or information resource, dataset, project portal, portal Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. human, mouse, genome, annotation, sequence, gene features, bio.tools is listed by: Debian
is listed by: bio.tools
is affiliated with: ENCODE
NHGRI 5U54HG004555;
Wellcome Trust WT098051
PMID:22955987 Free biotools:GENCODE https://bio.tools/GENCODE SCR_014966 ENCODE 2026-02-16 09:48:40 7700
tbl2asn
 
Resource Report
Resource Website
1+ mentions
tbl2asn (RRID:SCR_016636) data processing software, software application, software resource Software tool as a command-line program that automates the creation of sequence records for submission to GenBank. Records need no additional manual editing before submission. command, line, program, automate, creation, sequence, record, submit, data, GenBank has parent organization: NCBI Free, Freely available SCR_016636 2026-02-16 09:49:04 8
Gene-conservation-informed-contig-alignment
 
Resource Report
Resource Website
1+ mentions
Gene-conservation-informed-contig-alignment (RRID:SCR_017617) GCICA data processing software, software application, software resource Software tool for separation haplotigs from genome assembly. Method to separate haplotigs based on sequence similarity. Separation, haplotig, genome, assembly, sequence, similarity Free, Available for download, Freely available SCR_017617 2026-02-16 09:49:16 1
Sequencing of Idd regions in the NOD mouse genome
 
Resource Report
Resource Website
1+ mentions
Sequencing of Idd regions in the NOD mouse genome (RRID:SCR_001483) Sequencing of Idd regions in the NOD mouse genome data set, data or information resource, resource Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequences, such as their alignment, variation data and Ensembl gene coverage, can be obtained from the NOD mouse ftp site. genome, sequencing, genome sequencing, insulin-dependent diabetes, c57bl/6j, single nucleotide polymorphism, genetic variation, bacterial artificial chromosome, sequence, gene, animal model, clone, annotation, contig lists: VEGA
is listed by: NIDDK Information Network (dkNET)
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Type 1 diabetes, Diabetes NIAID AI 15416;
NIDDK ;
JDRF
PMID:23729657 Free, Freely available nlx_152738 http://www.sanger.ac.uk/resources/mouse/nod/ SCR_001483 Sequencing of Insulin-dependent diabetes regions in the NOD mouse genome 2026-02-16 09:45:29 1
UD Chick EST Project
 
Resource Report
Resource Website
10+ mentions
UD Chick EST Project (RRID:SCR_002236) material resource, biomaterial supply resource, cell repository THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created. gene, avian, cdna, chicken, clone, cytokine, dna, homology, immunology, mammalian, molecular, nucleotide, poultry, receptor, sequence, splenocyte, t cell is listed by: One Mind Biospecimen Bank Listing
has parent organization: University of Delaware; Delaware; USA
PMID:16554550 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-20971 SCR_002236 U.D. Chick EST Database, University of Delaware Chick EST Project, University of Delaware Chick EST Database 2026-02-16 09:45:46 18
SeqEM
 
Resource Report
Resource Website
1+ mentions
SeqEM (RRID:SCR_002021) software application, data processing software, sequence analysis software, data analysis software, algorithm resource, software resource, web application Online tool for utilizing a genotype calling algorithm for next-generation sequence data. genotype, algorithm, sequence, rna, dna, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Miami Miller School of Medicine; Florida; USA
PMID:20861027 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00074, biotools:seqem https://bio.tools/seqem SCR_002021 2026-02-16 09:45:42 1
RNA Ontology
 
Resource Report
Resource Website
1+ mentions
RNA Ontology (RRID:SCR_003470) RNAO ontology, data or information resource, controlled vocabulary An ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs. owl, obo, molecular structure, molecular, rna, sequence, alignment, structure, base pairing, base stacking, motif is listed by: BioPortal
is listed by: OBO
is listed by: Google Code
Free, Available for download, Freely available nlx_157566 http://purl.bioontology.org/ontology/RNAO
http://rnao.googlecode.com/svn/trunk/rnao.obo
SCR_003470 2026-02-16 09:46:09 1
Influenza Ontology
 
Resource Report
Resource Website
Influenza Ontology (RRID:SCR_003346) FLU ontology, data or information resource, controlled vocabulary An application ontology established by a collaborative group of influenza researchers that includes consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS) owl, health, pathological, organismal, cellular, sequence, surveillance is listed by: BioPortal
is listed by: OBO
is related to: Information Artifact Ontology
has parent organization: University of Maryland; Maryland; USA
Influenza Free, Freely available nlx_157440 http://purl.obolibrary.org/obo/flu.owl
http://influenzaontologywiki.igs.umaryland.edu/
http://purl.bioontology.org/ontology/FLU SCR_003346 2026-02-16 09:46:03 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
LAST
 
Resource Report
Resource Website
100+ mentions
LAST (RRID:SCR_006119) LAST software application, data processing software, data analysis service, analysis service resource, software resource, production service resource, service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. sequence alignment, align, vertebrate, genome, sequence, alignment, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: RecountDB
has parent organization: National Institute of Advanced Industrial Science and Technology
National Genome Research Network ;
INTEuropean Union Systems Institute ;
Japanese Ministry of Education Culture Sports Science and Technology MEXT
PMID:21209072
PMID:20144198
PMID:20110255
DOI:10.1093/nar/gkq010
THIS RESOURCE IS NO LONGER IN SERVICE nlx_151594, biotools:last, OMICS_15813 https://bio.tools/last
https://sources.debian.org/src/last-align/
SCR_006119 2026-02-16 09:46:37 397
FASTA
 
Resource Report
Resource Website
500+ mentions
FASTA (RRID:SCR_011819) FASTA software application, data processing software, sequence analysis software, data analysis software, software resource Software package for DNA and protein sequence alignment to find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. sequence, alignment, DNA, protein, similarity, searching is listed by: OMICtools
is listed by: SoftCite
has parent organization: European Bioinformatics Institute
Free, Freely available OMICS_00994 SCR_011819 Federal Acquisition STreamlining Act 2026-02-16 09:48:00 845
MacVector
 
Resource Report
Resource Website
1000+ mentions
MacVector (RRID:SCR_015700) software application, data processing software, sequence analysis software, data analysis software, software resource Software application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions. vector, sequence, sequence alignment, sequence editing, primer design, phylogenetic reconstruction, FASEB list Commercially available, Available for purchase, Runs on Mac OS, Free version available SCR_015700 2026-02-16 09:48:51 1496
Ariba
 
Resource Report
Resource Website
100+ mentions
Ariba (RRID:SCR_015976) software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst is listed by: Debian
is listed by: OMICtools
Wellcome Trust 206194;
Biotechnology and Biological Sciences Research Council BB/M014088/1
PMID:29177089
DOI:10.1099/mgen.0.000131
Free, Available for download, Freely available OMICS_17327 https://sources.debian.org/src/artemis/ SCR_015976 2026-02-16 09:48:55 197

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