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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SeqEM Resource Report Resource Website 1+ mentions |
SeqEM (RRID:SCR_002021) | software application, sequence analysis software, data processing software, algorithm resource, software resource, web application, data analysis software | 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 | 2026-02-15 09:18:13 | 1 | |||||||
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COnsensus-DEgenerate Hybride Oligonucleotide Primers Resource Report Resource Website 1+ mentions |
COnsensus-DEgenerate Hybride Oligonucleotide Primers (RRID:SCR_002875) | software application, data analysis service, data processing software, software resource, service resource, production service resource, analysis service resource, data analysis software | 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 | 2026-02-15 09:18:24 | 8 | ||||||||
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LAST Resource Report Resource Website 100+ mentions |
LAST (RRID:SCR_006119) | LAST | software application, data analysis service, software resource, data processing software, service resource, production service resource, analysis 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 | 2026-02-15 09:19:08 | 397 | |||||
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FASTA Resource Report Resource Website 500+ mentions |
FASTA (RRID:SCR_011819) | FASTA | software application, sequence analysis software, data processing software, software resource, data analysis software | 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 | 2026-02-15 09:20:24 | 845 | |||||||
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StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
the Cancer Prevention and Research Institute of Texas ; NHGRI R01 HG006677; NIGMS R01 GM105705; NHGRI R01 HG006102; NCI R01 CA120185; NCI R01 CA134292 |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie https://bio.tools/stringtie https://sources.debian.org/src/stringtie/ |
SCR_016323 | 2026-02-15 09:21:38 | 4072 | ||||||
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Hinge Resource Report Resource Website 1+ mentions |
Hinge (RRID:SCR_016135) | software application, sequence analysis software, data processing software, software resource, data analysis software | 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 | 2026-02-15 09:21:32 | 9 | |||||||
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FreeContact Resource Report Resource Website 10+ mentions |
FreeContact (RRID:SCR_016113) | software application, data processing software, software resource, alignment software, image analysis software | Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud). | protein, structure, prediction, sequence, analysis, fast, contact, alignment, multiple |
is listed by: OMICtools is related to: Debian |
Alexander von Humboldt Foundation ; German Ministry for Research and Education (BMBF: Bundesministerium fuer Bildung und Forschung) ; Research Council of Norway 208481 |
PMID:24669753 DOI:10.1186/1471-2105-15-85 |
Open source, Free, Available for download | OMICS_03520 | https://rostlab.org/owiki/index.php/FreeContact https://sources.debian.org/src/libfreecontact-perl/ |
SCR_016113 | 2026-02-15 09:21:02 | 21 | ||||||
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QModeling Resource Report Resource Website 1+ mentions |
QModeling (RRID:SCR_016358) | software application, data processing software, software resource, image analysis software, software toolkit, data analysis software | Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences. | statistical, parametric, mapping, reference, region, kinetic, model, dynamic, analysis, brain, data, imaging, sequence |
is related to: University of Malaga; Andalusia; Spain is related to: MATLAB |
DOI:10.1007/s12021-018-9384-y | Free, Available for download, Available after registration | SCR_016358 | 2026-02-15 09:21:51 | 1 | |||||||||
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NanoPipe Resource Report Resource Website 1+ mentions |
NanoPipe (RRID:SCR_016852) | NanoPipe | data analysis service, software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms. | analysis, MinION, long, sequence, read, Oxford Nanopore, alignment, target, statistics, polymorphism, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Muenster; Muenster; Germany |
Institute of Bioinformatics Muenster ; Germany |
PMID:30689855 | Free, Available for download, Freely Available | biotools:NanoPipe | https://github.com/IOB-Muenster/nanopipe2 https://bio.tools/NanoPipe |
SCR_016852 | NanoPipe, nanopipe2 | 2026-02-15 09:21:49 | 5 | ||||
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ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | software application, sequence analysis software, data processing software, software resource, data analysis software | 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 |
Wellcome Trust WT082930MA; National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882 |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-02-15 09:21:30 | 8 | ||||||
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GeMoMa Resource Report Resource Website 100+ mentions |
GeMoMa (RRID:SCR_017646) | software application, simulation software, software resource | Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species. | Homology, based, gene, prediction, model, target, evolutionary, related, reference, species, sequence, conservation, intron, position, RNAseq, data, protein, coding, transcript, bio.tools |
is listed by: bio.tools is listed by: Debian works with: GUSHR |
PMID:31020559 | Free, Available for download, Freely available | biotools:gemoma | https://bio.tools/gemoma | SCR_017646 | Gene Model Mapper | 2026-02-15 09:21:23 | 135 | ||||||
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PseudoFuN Resource Report Resource Website 1+ mentions |
PseudoFuN (RRID:SCR_017095) | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Software as database and query tool for homologous pseudogene and coding gene families. Collection of human pseudogenes and gene associations. Supports search, graphical visualization and functional analysis of pseudogenes and coding genes based on PGG families. | gene, pseudogene, sequence, homology, regulatory, network, miRNA, coexpression, noncoding, RNA, TCGA, cancer |
has parent organization: Ohio State University; Ohio; USA has parent organization: Indiana University School of Medicine; Indiana; USA |
NLM T15 LM011270 | Free, Freely available | https://github.com/yanzhanglab/PseudoFuN_app | SCR_017095 | Pseudogene Functional Networks | 2026-02-15 09:21:56 | 2 | |||||||
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Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome Resource Report Resource Website |
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) | HEFalMp | data or information resource, database, service resource | HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool. | human, map, gene, functional, pathway, disease, genomic, analysis, microarray, dna, protein, sequence | has parent organization: Princeton University; New Jersey; USA | New Jersey Commission on Cancer Research ; PhRMA Foundation 2007RSGl9572; NIGMS R01 GM071966; NSF DBI-0546275; NSF IIS-0513552; NHGRI T32 HG003284; NIGMS P50 GM071508 |
PMID:19246570 | nif-0000-37186 | SCR_003506 | Human Experimental / FunctionAL MaPper, Human Experimental/FunctionAL MaPper | 2026-02-15 09:18:31 | 0 | ||||||
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Coddle-Codons Optimized to Discover Deleterious LEsions Resource Report Resource Website 10+ mentions |
Coddle-Codons Optimized to Discover Deleterious LEsions (RRID:SCR_003003) | CODDLE | service resource, analysis service resource, data analysis service, production service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Web-accessible program that identifies the region(s) of a user-selected gene and of its coding sequence (CDS) where the anticipated point mutations are most likely to result in deleterious effects on the gene's function. CODDLe separately handles 1) the prediction of changes which should truncate the protein and destabilize the RNA - nonsense changes and splice junction changes, and 2) the prediction of missense changes which should alter function of the gene product - those in conserved amino acid blocks in the CDS. Because the region(s) identified will be PCR amplified by the user and that amplicon will be used for polymorphism discovery, the application delivers primer pairs selected by Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998)Primer3.) After selecting a primer pair, CODDLe returns a window with the selected amplicon and tabulates the effects of all possible polymorphisms which could be detected in that amplicon. CODDLe will not identify the regions of a gene where polymorphisms are most likely to be discovered. Others have shown that naturally occurring SNPs are found more often in the untranslated regions of a gene. | codon, deleterious lesion, gene, coding, sequence, mutation, primer, protein sequence, cdna, sequence alignment, coding sequence |
is listed by: 3DVC has parent organization: Fred Hutchinson Cancer Center |
DOE ; Office of Energy Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30262 | SCR_003003 | Choosing codons to Optimize Discovery of Deleterious Lesions, Codons Optimized to Discover Deleterious LEsions | 2026-02-15 09:18:27 | 16 | ||||||
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BiSearch: Primer Design and Search Tool Resource Report Resource Website 50+ mentions |
BiSearch: Primer Design and Search Tool (RRID:SCR_002980) | BiSearch | service resource, analysis service resource, data analysis service, production 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 | 2026-02-15 09:18:27 | 50 | |||||||
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TFSEARCH: Searching Transcription Factor Binding Sites Resource Report Resource Website 100+ mentions |
TFSEARCH: Searching Transcription Factor Binding Sites (RRID:SCR_004262) | service resource, analysis service resource, data analysis service, production 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 | 2026-02-15 09:18:43 | 214 | |||||||
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MG-RAST Resource Report Resource Website 1000+ mentions |
MG-RAST (RRID:SCR_004814) | MG RAST | service resource, analysis service resource, data analysis service, production service resource | An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples. | metagenome, base pair, sequence, phylogenetic, functional analysis, data sharing, metadata, protein, micro biome, analysis platform, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: Argonne National Laboratory |
NIAID contract HHSN272200900040C; DOE contract DE-AC02-06CH11357 |
PMID:18803844 | Acknowledgement requested, Public, Account required | OMICS_01456, biotools:mg-rast | http://metagenomics.nmpdr.org https://bio.tools/mg-rast |
SCR_004814 | The Metagenomics RAST server, Metagenomics RAST, MG-RAST - metagenomics analysis server | 2026-02-15 09:18:49 | 1137 | ||||
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Human Splicing Finder Resource Report Resource Website 500+ mentions |
Human Splicing Finder (RRID:SCR_005181) | HSF | service resource, analysis service resource, data analysis service, production service resource | Software tool to help study pre-mRNA splicing and to better understand intronic and exonic mutations leading to splicing defects. To calculate the consensus values of potential splice sites and search for branch points, new algorithms were developed. Furthermore, they have integrated all available matrices to identify exonic and intronic motifs, as well as new matrices to identify hnRNP A1, Tra2-? and 9G8. | splicing, mutation, splicing signal, sequence, transcript, nucleotide, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Ensembl has parent organization: National Institute of Health and Medical Research; Rennes; France |
PMID:19339519 | Acknowledgement requested | biotools:human_splicing_finder, OMICS_00176 | https://bio.tools/human_splicing_finder | http://www.umd.be/HSF/ | SCR_005181 | 2026-02-15 09:19:02 | 963 | |||||
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PRED-CLASS Resource Report Resource Website |
PRED-CLASS (RRID:SCR_006216) | PRED-CLASS | service resource, analysis service resource, data analysis service, production service resource | A system of cascading neural networks that classifies any protein, given its amino acid sequence alone, into one of four possible classes: membrane, globular, fibrous, mixed. | classification, protein, fibrous, globular, protein class, membrane, sequence, algorithm, protein classification, neural network, transmembrane, genome annotation, genome-wide analysis |
is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
European Union ERBFMRXCT960019 | PMID:11455609 | nlx_151762 | SCR_006216 | PRED-CLASS - Classification of proteins into one of four possible classes | 2026-02-15 09:19:11 | 0 | ||||||
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ProbeExplorer Resource Report Resource Website |
ProbeExplorer (RRID:SCR_007116) | ProbeExplorer | service resource, analysis service resource, data analysis service, production service resource | Probe Explorer is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query. Platform: Online tool | bioinformatics, microarray, oligonucleotide probe, transcript, genomic, genome, transcriptome, alignment, affymetrix, probe sequence, dna, protein, sequence, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Salamanca; Salamanca; Spain |
Open unspecified license - Free for academic use | nlx_149275 | SCR_007116 | Probe Explorer | 2026-02-15 09:19:27 | 0 |
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