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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.

(last updated: Aug 10, 2019)

Physical Resource or Software Tool Software

881 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
LiGraphResource, analysis service resource, data analysis service, service resource, production service resourceService that generates schematic drawings of oligosaccharides which are often used to display glycan structure.carbohydrate, iupac, notation, ascii, graph, nomenclature, oligosaccharide, glycan, structure, sugarSCR_000385(LiGraph, RRID:SCR_000385)German Cancer Research Center listed by: glycosciences.deLast checked upnlx_152884
UCSCinResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Beta software used to align and browse a genome.genomeSCR_000571(UCSCin, RRID:SCR_000571)University of Toronto; Ontario; Canada Last checked downnlx_144379
JCVI CMRResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase of all of the publicly available, complete prokaryotic genomes. In addition to having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes. CMR offers a wide variety of tools and resources, all of which are available off of our menu bar at the top of each page. Below is an explanation and link for each of these menu options. * Genome Tools: Find organism lists as well as summary information and analyses for selected genomes. * Searches: Search CMR for genes, genomes, sequence regions, and evidence. * Comparative Tools: Compare multiple genomes based on a variety of criteria, including sequence homology and gene attributes. SNP data is also found under this menu. * Lists: Select and download gene, evidence, and genomic element lists. * Downloads: Download gene sequences or attributes for CMR organisms, or go to our FTP site. * Carts: Select genome preferences from our Genome Cart or download your Gene Cart genes. The Omniome is the relational database underlying the CMR and it holds all of the annotation for each of the CMR genomes, including DNA sequences, proteins, RNA genes and many other types of features. Associated with each of these DNA features in the Omniome are the feature coordinates, nucleotide and protein sequences (where appropriate), and the DNA molecule and organism with which the feature is associated. Also available are evidence types associated with annotation such as HMMs, BLAST, InterPro, COG, and Prosite, as well as individual gene attributes. In addition, the database stores identifiers from other centers such as GenBank and SwissProt, as well as manually curated information on each genome or each DNA molecule including website links. Also stored in the Omniome are precomputed homology data, called All vs All searches, used throughout the CMR for comparative analysis.microbial, prokaryotic, genome, annotation, dna sequence, protein, rna gene, blastSCR_005398(JCVI CMR, RRID:SCR_005398)J. Craig Venter Institute DOE, NIAID, NSFrelated to: AmiGO, used by: NIF Data FederationLast checked upnif-0000-03555
ConBBPREDResource, analysis service resource, data analysis service, service resource, production service resourceA web tool for the Consensus Prediction of TransMembrane Beta-Barrel Proteins. Prediction of the transmembrane strands and topology of beta-barrel outer membrane proteins is of interest in current bioinformatics research. Several methods have been applied so far for this task, utilizing different algorithmic techniques and a number of freely available predictors exist. The methods can be grossly divided to those based on Hidden Markov Models (HMMs), on Neural Networks (NNs) and on Support Vector Machines (SVMs). In this work, we compare the different available methods for topology prediction of beta-barrel outer membrane proteins. We evaluate their performance on a non-redundant dataset of 20 beta-barrel outer membrane proteins of gram-negative bacteria, with structures known at atomic resolution. Also, we describe, for the first time, an effective way to combine the individual predictors, at will, to a single consensus prediction method. We assess the statistical significance of the performance of each prediction scheme and conclude that Hidden Markov Model based methods, HMM-B2TMR, ProfTMB and PRED-TMBB, are currently the best predictors, according to either the per-residue accuracy, the segments overlap measure (SOV) or the total number of proteins with correctly predicted topologies in the test set. Furthermore, we show that the available predictors perform better when only transmembrane beta-barrel domains are used for prediction, rather than the precursor full-length sequences, even though the HMM-based predictors are not influenced significantly. The consensus prediction method performs significantly better than each individual available predictor, since it increases the accuracy up to 4% regarding SOV and up to 15% in correctly predicted topologies.predict, topology, beta-barrel outer membrane protein, outer membrane protein, protein, consensus prediction, gram-negative bacteria, transmembrane, beta-barrel proteinSCR_006194(ConBBPRED, RRID:SCR_006194)University of Athens Biophysics and Bioinformatics Laboratory Greek Ministry of National Education and Religious AffairsPMID:15647112Last checked upnlx_151740
ArrayPipeResource, analysis service resource, data analysis service, service resource, production service resourceA flexible tool for visualizing and analyzing your two-colour microarray slides.SCR_010934(ArrayPipe, RRID:SCR_010934)listed by: OMICtoolsLast checked upOMICS_00744
Isofinder: Isochore Computational PredictionResource, analysis service resource, data analysis service, service resource, production service resourceIsofinder is an algorithm running on the web able to predict isochores at the sequence level. Isochores are long genome segments homogeneous in G+C. The algorithm works by moving a sliding pointer from left to right along the DNA sequence and computing the mean G+C values to the left and to the right of the pointer at each point. Additionally, the program checks whether this significance exceeds a probability threshold. If so, the sequence is cut at this point into two subsequences; otherwise, the sequence remains undivided. The procedure continues recursively for each of the two resulting subsequences created by each cut. This leads to the decomposition of a chromosome sequence into long homogeneous genome regions (LHGRs) with well-defined mean G+C contents, each significantly different from the G+C contents of the adjacent LHGRs. Most LHGRs can be identified with Bernardi''s isochores, given their correlation with biological features such as gene density, SINE and LINE (short, long interspersed repetitive elements) densities, recombination rate or single nucleotide polymorphism variability. The resulting isochore maps are available at, and also at the UCSC Genome Browser ( Sponsors: Isofinder is funded by Universidad de Granada, Spain.algorithm, chromosome, dna, genome, heterogeneous, homogeneous, isochore, segment, sequence, single nucleotide polymorphism, snp, statisticSCR_008342(Isofinder: Isochore Computational Prediction, RRID:SCR_008342)University of Granada; Granada; Spain Last checked upnif-0000-25208
DegustResource, software resource, analysis service resource, data analysis service, service resource, production service resourceAn interactive web tool for visualizing differential gene expression data.differential gene expression, differential expression, gene expression, visualizationSCR_001878(Degust, RRID:SCR_001878)Monash University; Melbourne; Australia listed by: OMICtoolsLast checked upOMICS_01934
miRDBResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceAn online database for miRNA target prediction and functional annotations.mirna, target, pathwaySCR_010848(miRDB, RRID:SCR_010848)listed by: OMICtoolsReferences (2)Last checked upOMICS_00403
ExpressYourselfResource, analysis service resource, data analysis service, service resource, production service resourceA fully integrated platform for processing microarray data.SCR_008881(ExpressYourself, RRID:SCR_008881)listed by: OMICtoolsLast checked upOMICS_00755
StSNPResource, analysis service resource, data analysis service, service resource, production service resourceA web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.SCR_005417(StSNP, RRID:SCR_005417)listed by: OMICtoolsLast checked upOMICS_00138
SynGOResource, data analysis service, production service resource, analysis service resource, service resource, ontology, controlled vocabulary, data or information resourceEvidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotationSCR_017330(SynGO, RRID:SCR_017330)CERCA Program/Generalitat de Catalunya, European Union, German Federal Ministry of Education and Research, NINDS, Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvarduses: Gene Ontology, submitted by: Neuroscience Information FrameworkPMID:31171447Last checked up
Phalanx Biotech GroupResource, analysis service resource, data analysis service, service resource, group, production service resourceGroup service that provides expression profiling products and services. They manufacture DNA microarrays for gene expression and microRNA profiling.expression profiling service provider, genomics analysis facilitySCR_002717(Phalanx Biotech Group, RRID:SCR_002717)listed by: Science ExchangeLast checked upSciEx_13118
FunSimMatResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceFunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online toolfunctional similarity value, protein family, protein similarity, semantic similarity value, similarity value, functional similarity, disease gene candidate prioritization, disease, protein, protein family, disease candidate prioritization, semantic similarity, gene ontology, visualization, annotation, database or data warehouseSCR_002729(FunSimMat, RRID:SCR_002729)Max-Planck-Institute for Informatics; Saarbrucken; Germany European Union, German National Genome Research Network, Klinische Forschergrupperelated to: Gene Ontology, listed by: Gene Ontology ToolsReferences (2)Last checked upnif-0000-02860
COnsensus-DEgenerate Hybride Oligonucleotide PrimersResource, data analysis service, data analysis software, data processing software, production service resource, analysis service resource, software application, service resource, software resourceThis 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.fractionation, gel, 3', amplification, clone, dna, genome, homolog, human, hybrid, molecule, oligonucleotide, pcr, plant, primer, protein, sequence, transcriptase-methyltransferaseSCR_002875(COnsensus-DEgenerate Hybride Oligonucleotide Primers, RRID:SCR_002875)University of Washington; Seattle; USA related to: OMICtoolsLast checked upnif-0000-25557
ISFinderResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, data repository, data or information resourceDatabase of a list of insertion sequences isolated from eubacteria and archaea. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences. Although most of the entries have been identified as individual elements, a growing number are included from their description in sequenced bacterial genomes. The search engine permits the retrieval and display of individual and groups of ISs based on a combination of their general features. Two levels of search are available. The simple search option enables the user to sort elements using a limited number of basic items whereas the extensive search offers an additional set of possibilities such as comparisons of the sequences of terminal inverted repeats and a variety of different layout displays. Built in links are provided to: the EMBL sequence database, the NCBI taxonomy database and to the ESF plasmid database. At present, only individual sequences can be downloaded one by one for comparison. An on-line BLAST facility is available and in future versions direct access to additional analytical tools will be provided on line. Direct submission of ISs is encouraged using the on-line form provided.insertion sequence, insertion, sequence, blast, dna, protein sequenceSCR_003020(ISFinder, RRID:SCR_003020)Paul Sabatier University - Toulouse III; Toulouse; France CNRSLast checked downnif-0000-03050
GENEWIZOrganization, analysis service resource, service resource, production service resource, material analysis serviceCommercial organization for research and development genomics services and technical support to researchers.genomics, research support, research services, companySCR_003177(GENEWIZ, RRID:SCR_003177)Last checked upnif-0000-30606
MultiLocResource, analysis service resource, software resource, data analysis service, service resource, production service resourceAn extensive high-performance subcellular protein localization prediction system that incorporates phylogenetic profiles and Gene Ontology terms to yield higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. A downloadable version of MultiLoc2 for local use is also available.subcellular localization, proteinSCR_003151(MultiLoc, RRID:SCR_003151)University of Tubingen; Tubingen; Germany listed by: OMICtoolsPMID:19723330Last checked upOMICS_01628
MAGIResource, analysis service resource, data analysis service, service resource, production service resourceA web service for fast microRNA-Seq data analysis in a GPU infrastructure.fastq, c, perl, php, software program, gpu/cudaSCR_003360(MAGI, RRID:SCR_003360)University of California at San Diego; California; USA listed by: OMICtoolsPMID:24907367Last checked upOMICS_04636
Banyan BiomarkersResource, data analysis service, assessment test provider, production service resource, analysis service resource, service resource, material resourceBanyan Biomarkers was founded in 2002 by Ron Hayes, PhD , Kevin Wang, PhD, and Nancy Denslow, PhD to create the first Point of Care (POC) Blood Test to diagnose traumatic brain injury (TBI) and to diagnose neurological diseases. Initially inspired by research conducted at the University of Florida and The Evelyn F. and William McKnight Brain Institute, Banyan Biomarkers has made significant progress in developing and clinically validating novel enzyme linked immunosorbent assays (ELISAs) for traumatic brain injury (TBI). Banyan scientists have created an extensive pipeline of potential biomarkers and the company has a robust intellectual property portfolio. Jackson Streeter, Banyan''s CEO, has extensive experience in development of medical devices for acute brain injury. Currently no blood test exists for use by physicians to detect the presence and severity of brain trauma. Banyan Biomarkers'' research has identified unique and proprietary biomarkers present in the patient''s blood following injury to the brain. The detection and quantification of these biomarkers may provide early indications of brain trauma essential for earlier intervention and management. Banyan Biomarkers, Inc. offers preclinical and clinical sample analyses with a proven panel of neurological, psychiatric, neurodegenerative disease, and organ toxicity biomarker assays. The company provides analytical services to a wide range of customers including pharmaceutical companies, biotechnology companies and investigators at academic research institutes.traumatic brain injury, blood test, human, brain, stroke, liver injury, biomarker, immunoassay, neurodegenerative disease, neurological disorder, mental disease, neuroinflammation, microglial activation, apoptosis, necrosis, hepatoxicity, in vitro, diagnostic test, enzyme linked immunosorbent assay, one mind tbiSCR_004515(Banyan Biomarkers, RRID:SCR_004515)Last checked upnlx_143797
PANTHER Evolutionary analysis of coding SNPsResource, data analysis service, data analysis software, data processing software, production service resource, analysis service resource, software application, service resource, software resourceData analysis service that estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. To analyze many SNPs, download the PANTHER Coding Snp Analysis tool from the downloads page.SCR_005145(PANTHER Evolutionary analysis of coding SNPs, RRID:SCR_005145)PANTHER listed by: OMICtoolsPMID:23193289Last checked upOMICS_00135
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