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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pecan Resource Report Resource Website 50+ mentions |
Pecan (RRID:SCR_001909) | software resource | A Java consistency based multiple sequence alignment software program. | java, sequence, alignment, consistency, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA |
PMID:18849524 | Free, Available for download, Freely available | OMICS_03739, biotools:pecan | http://hgwdev.cse.ucsc.edu/~benedict/code/Pecan.html https://bio.tools/pecan |
SCR_001909 | 2026-02-14 02:00:14 | 50 | |||||||
|
CHAoS Resource Report Resource Website 10+ mentions |
CHAoS (RRID:SCR_005174) | CHAoS | software resource | A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization. | annotation, analysis, visualization, variant, high-throughput sequencing, perl, population genetic, transcript, positional record, sequence, motif, genotype |
is listed by: OMICtools has parent organization: Wellcome Trust Centre for Human Genetics |
GNU General Public License, v2 | OMICS_00170 | SCR_005174 | chaos - Annotation analysis and visualization of variants from high-throughput sequencing experiments | 2026-02-14 02:00:50 | 26 | |||||||
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READSCAN Resource Report Resource Website 1+ mentions |
READSCAN (RRID:SCR_005204) | READSCAN | software resource | A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. | pathgen, genome, sequence, high-throughput sequence, align, read, host, microbe, virus, taxon, simulation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:23193222 | OMICS_00222, biotools:readscan | https://bio.tools/readscan | SCR_005204 | 2026-02-14 02:00:52 | 5 | |||||||
|
LookSeq Resource Report Resource Website 1+ mentions |
LookSeq (RRID:SCR_005625) | LookSeq | software resource | A web-based application for alignment visualization, browsing and analysis of genome sequence data. | alignment, visualization, browsing, analysis, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00886 | SCR_005625 | 2026-02-14 02:01:08 | 5 | |||||||||
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MedBlast Resource Report Resource Website 1+ mentions |
MedBlast (RRID:SCR_008202) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs. | gene, article, biological, data, genome, genomic, homolog, literature, medline interfaces, mining, molecular, protein, sequence, specie | National Natural Science Foundation of China 39990600-03; Knowledge Innovation Program of the Chinese Academy of Sciences KSCX2-2-07; Knowledge Innovation Program of the Chinese Academy of Sciences KJCX1-08 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21253 | SCR_008202 | MedBlast | 2026-02-14 02:01:37 | 1 | ||||||||
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Joint Center for Structural Genomics Resource Report Resource Website 50+ mentions |
Joint Center for Structural Genomics (RRID:SCR_008251) | JCSG | institution | The JCSG is a multi-institutional consortium that aims to explore the expanding protein universe to find new challenges and opportunities to significantly contribute to new biology, chemistry and medicine through development of HT approaches to structural genomics. The mission of JCSG is to to operate a robust HT protein structure determination pipeline as a large-scale production center for PSI-2. A major goal is to ensure that innovative high-throughput approaches are developed that advance not only structural genomics, but also structural biology in general, via investigation of large numbers of high-value structures that populate protein fold and family space and by increasing the efficiency of structure determination at substantially reduced cost. The JCSG centralizes each core activity into single dedicated sites, each handling distinct, but interconnected objectives. This unique approach allows each specialized group to focus on its own area of expertise and provides well-defined interfaces among the groups. In addition, this approach addresses the requirements for the scalability needed to process large numbers of targets at a greatly reduced cost per target. JCSG production groups are: - Administrative Core - Bioinformatics Core - Crystallomics Core - Structure Determination Core - NMR Core JCSG is deeply committed to the development of new technologies that facilitate high throughput structural genomics. The areas of development include hardware, software, new experimental methods, and adaptation of existing technologies to advance genome research. In the hardware arena, their commitment is to the development of technologies that accelerate structure solution by increasing throughput rates at every stage of the production pipeline. Therefore, one major area of hardware development has been the implementation of robotics. In the software arena, they have developed enterprise resource software that track success, failures, and sample histories from target selection to PDB deposition, annotation and target management tools, and helper applications aimed at facilitating and automating multiple steps in the pipeline. Sponsors: The Joint Center for Structural Genomics is funded by the National Institute of General Medical Sciences (NIGMS), as part of the second phase of the Protein Structure Initiative (PSI) of the National Institutes of Health (U54 GM074898). | exclusion chromatography, expression, fine-structure spectroscopy, fold, absorption, affinity, bacterial, baculovirus, bioinformatics, biology, biophysical, cell, chemistry, cloning, crystallization, crystallomics, differential scanning calorimetry, diffraction, domain, genomic, gnfuge, growth, hardware, ief gel electrophoresis, macromoleuclar, medicine, microexpression, mouse, nmr, optical density, physicochemical, protein, purification, recombinatorial, robotics, sds-page, sequence, software, structural, structural biology, structure, technology, thermocycler, topoisomerase, tryptic mass spectrometry, uv/vis absorbance scan, x-ray |
has parent organization: University of California at San Diego; California; USA has parent organization: Scripps Research Institute has parent organization: Sanford Burnham Prebys Medical Discovery Institute has parent organization: Stanford University; Stanford; California |
nif-0000-22295, grid.419677.a | https://ror.org/00exr1241 | SCR_008251 | JCSG | 2026-02-14 02:01:35 | 99 | |||||||
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Affymetrix Power Tools Resource Report Resource Website 10+ mentions |
Affymetrix Power Tools (RRID:SCR_008401) | software resource | Affymetrix Power Tools (APT) are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChip arrays. APT programs are intended for power users who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality. APT provides platform for developing and deploying new algorithms without waiting for the GUI implementations. This resource is supported by Affymetrix, Inc. | Affymetrix, Inc., Genomics, Clinical, Study, Bioinformatic, Windows, MacOS, Linux, resource, Data, Normalization, Sequence, Annotation, Gene, Expression, Pattern, Motif, Inference, Toolkit, Model, Fitting, Algorithm |
has parent organization: Affymetrix has parent organization: Affymetrix |
nif-0000-30070 | https://www.affymetrix.com/support/developer/powertools/changelog/install.html https://media.affymetrix.com/support/developer/powertools/changelog/index.html |
http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx | SCR_008401 | APT | 2026-02-14 02:01:38 | 30 | |||||||
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CD-HIT-OTU Resource Report Resource Website 50+ mentions |
CD-HIT-OTU (RRID:SCR_006983) | CD-HIT-OTU | software resource | Data analysis service and software program that perform Operantional Taxonomic Units (OTUs) finding. It uses a three-step clustering for identifying OTUs. The first-step clustering is raw read filtering and trimming. The second step is error-free reads picking.. At the last step, OTU clustering is done at different distanct cutoffs (0.01, 0.02, 0.03... 0.12). | 454, read, illumina, rrna, fasta, metagenome, sequence, clustering, metagenomics, next-generation sequencing, protein |
is listed by: OMICtools has parent organization: CD-HIT |
PMID:22772836 PMID:21899761 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01441 | SCR_006983 | 2026-02-14 02:01:26 | 88 | |||||||
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REBASE Resource Report Resource Website 100+ mentions |
REBASE (RRID:SCR_007886) | REBASE | data or information resource, database | Database of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Several tools are available including REBsites, BLAST against REBASE, NEBcutter and REBpredictor. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. Users may submit new enzyme and/or sequence information, recommend references, or send them corrections to existing data. The contents of REBASE may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email., | endonuclease, enzyme, genome, archaeal, bacterial, cleavage, crystal, dna, individual protein family databases, isochizomer, methylation, methyltransferase, modification, protein, recognition, restriction, restriction enzyme, sensitivity, sequence, site, methylase, cleavage site, restriction-modification, blast, FASEB list |
has parent organization: New England Biolabs works with: Webcutter |
New England Biolabs Inc ; NLM LM04971 |
PMID:19846593 PMID:17202163 |
r3d100012171, nif-0000-03391 | http://rebase.neb.com https://doi.org/10.17616/R3J930 |
http://www.neb.com/rebase | SCR_007886 | The Restriction Enzyme Database, Restriction Enzyme Database | 2026-02-14 02:01:35 | 246 | ||||
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Wellcome Trust Sanger Institute; Hinxton; United Kingdom Resource Report Resource Website 500+ mentions |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) | WTSI, Sanger | institution | Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request. | research, genome, sequence, human, health, project, global, data, treatment, therapy |
is listed by: re3data.org is affiliated with: Open Targets is related to: Clonalframe is related to: ClonalOrigin is related to: TraCeR is parent organization of: ILLUMINUS is parent organization of: ARNIE is parent organization of: Sequence Search and Alignment by Hashing Algorithm is parent organization of: Sequencing of Idd regions in the NOD mouse genome is parent organization of: CAROL is parent organization of: DINDEL is parent organization of: Wellcome Trust Case Control Consortium is parent organization of: OLORIN is parent organization of: Exomiser is parent organization of: COSMIC - Catalogue Of Somatic Mutations In Cancer is parent organization of: GeneDB is parent organization of: Breast Cancer Somatic Genetics Study is parent organization of: Artemis: Genome Browser and Annotation Tool is parent organization of: ACT: Artemis Comparison Tool is parent organization of: Alien hunter is parent organization of: Pfam is parent organization of: DNAPlotter is parent organization of: VAGrENT is parent organization of: SMALT is parent organization of: LookSeq is parent organization of: ZMP is parent organization of: Deciphering Developmental Disorders is parent organization of: Sanger Mouse Resources Portal is parent organization of: SpliceDB is parent organization of: DECIPHER is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: Genes to Cognition: Neuroscience Research Programme is parent organization of: MEROPS is parent organization of: Rfam is parent organization of: VEGA is parent organization of: Bacterial Genomes is parent organization of: Caenorhabditis Genome Sequencing Projects is parent organization of: D. rerio Blast Server is parent organization of: Fungi Sequencing Projects is parent organization of: PEER is parent organization of: Alfresco - FRont-End for Sequence COmparison is parent organization of: AutoCSA (Automatic Comparative Sequence Analysis) is parent organization of: AceDB is parent organization of: CnD is parent organization of: Genomics of Drug Sensitivity in Cancer is parent organization of: Zebrafish Genome Project is parent organization of: Tree families database is parent organization of: Ensembl is parent organization of: BamView is parent organization of: SVMerge is parent organization of: RetroSeq is parent organization of: Consensus CDS is parent organization of: WormBase is parent organization of: Belvu is parent organization of: Bio-tradis is parent organization of: Blixem is parent organization of: Dotter is parent organization of: Exonerate is parent organization of: Fastaq is parent organization of: Gubbins is parent organization of: CellPhoneDB is parent organization of: Ensembl Metazoa is parent organization of: Scmap is parent organization of: Scfind is parent organization of: Recognition of Errors in Assemblies using Paired Reads is parent organization of: SAMTOOLS is parent organization of: Cell Model Passports |
Wellcome Trust | ISNI: 0000 0004 0606 5382, nlx_91258, grid.10306.34, Wikidata: Q1142544 | https://ror.org/05cy4wa09 | SCR_011784 | Wellcome Trust Sanger Institute, Genome Research Limited, The Wellcome Sanger Institute, Sanger Institute, Wellcome Trust Sanger Institute Genome Research Limited | 2026-02-14 02:02:04 | 527 | ||||||
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GASiC Resource Report Resource Website 1+ mentions |
GASiC (RRID:SCR_006765) | GASiC | software resource | A method to correct read alignment results for the ambiguities imposed by similarities of genomes. | metagenome, genome, sequence, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:22941661 DOI:10.1093/nar/gks803 |
BSD License | OMICS_01437 | https://sources.debian.org/src/gasic/ | SCR_006765 | GASiC - Genome Abundance Similarity Correction, Genome Abundance Similarity Correction | 2026-02-14 02:01:15 | 3 | |||||
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T4-like genome database Resource Report Resource Website 10+ mentions |
T4-like genome database (RRID:SCR_005367) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of information on bacterial phages. It contains multiple phage genomes, which users can BLAST and MegaBLAST, and also hosts a Phage Forum in which users can discuss phage data. Interactive browsing of completed phage genomes is available using the program. The browser allows users to scan the genome for particular features and to download sequence information plus analyses of those features. Views of the genome are generated showing named genes BLAST similarities to other phages predicted tRNAs and other sequence features. | electron micrograph, genbank data, alignment to ortholog, blast server, dna sequence, genomics database, hydropathy plot, interactive sequence, non-vertebrate, pfam protein domain, protein sequence, protein statistics, sequence, t4-like bacteriophage genome, tulane t4-like sequencing project, viral genome database | has parent organization: Tulane University; Louisiana; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03532 | http://phage.ggc.edu/ | SCR_005367 | T4-like genome database | 2026-02-14 02:06:27 | 14 | |||||||
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Plant Genome Resource at JGI Resource Report Resource Website |
Plant Genome Resource at JGI (RRID:SCR_005315) | JGI Plant Genomics Program | data or information resource, database | The goal of the DOE JGI Plant Genome Program is to shed light on the fundamental biology of photosynthesis and transduction of solar to chemical energy. Other areas of interest include characterizing: * Ecosystems and the role of terrestrial plants and oceanic phytoplankton-in carbon sequestration. * The role of plants in coping with toxic pollutants in soils by hyper-accumulation and detoxification. * Feedstocks for biofuels, e.g., biodiesel from soybean; cellulosic ethanol from perennial grasses. * The ability to respond to environmental change (e.g., loss of diversity from monoculture produces vulnerabilities; nitrogen fixing nodules in legumes reduce fertilizer need). * The generation of useful secondary metabolites (produced largely for disease resistance)- for positive/negative control in agriculture, with attendant influence on global carbon cycle. The Plant Genome Program accomplishes the above through the following activities: # Sequence. Produce genome sequences of key plant (and algal) species to accelerate biofuel development and understand response to climate change. # Function. Develop datasets (and synthetic biology tools) to elucidate functional elements in plant genomes, with special focus on handful of flagship genomes. # Variation. Characterize natural genomic variation in plants (and their associated microbiomes), and relate to biofuel sustainability and adaptation to climate change. # Integration. Provide a centralized hub for the retrieval and deep integrated analysis of plant genome datasets. | plant, genomics, genome, photosynthesis, sequence | has parent organization: DOE Joint Genome Institute | DOE | nlx_144370 | SCR_005315 | Plant Genomics Program at JGI, DOE JGI Plant Genome Program, Plant Genomics Program - Capturing Light to Fuel Our Future | 2026-02-14 02:06:26 | 0 | |||||||
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STRING Resource Report Resource Website 10000+ mentions |
STRING (RRID:SCR_005223) | STRING | data or information resource, database | Database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations and are derived from four sources: Genomic Context, High-throughput experiments, (Conserved) Coexpression, and previous knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently covers 5''214''234 proteins from 1133 organisms. (2013) | protein association, protein functional association, protein interaction, protein-protein interaction, protein, sequence, protein sequence, interaction, gene, FASEB list |
is used by: MobiDB is used by: PAXdb is listed by: Nuclear Receptor Signaling Atlas is listed by: NIDDK Information Network (dkNET) is related to: Biomine is related to: PSICQUIC Registry is related to: ShinyGO has parent organization: European Molecular Biology Laboratory has plug in: Cytoscape StringApp |
BMBF ; European Union FP6 ; EMBO ; ProBioC ; Swiss Institute of Bioinformatics |
PMID:23203871 PMID:21045058 PMID:18940858 PMID:17098935 PMID:15608232 PMID:12519996 |
nif-0000-03503, r3d100010604 | https://doi.org/10.17616/R3VS40 | SCR_005223 | Search Tool for the Retrieval of Interacting Genes/Proteins, STRING - Known and Predicted Protein-Protein Interactions | 2026-02-14 02:06:23 | 29246 | |||||
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MIPModDB Resource Report Resource Website 1+ mentions |
MIPModDB (RRID:SCR_006058) | MIPModDB | data or information resource, database | This is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. The nearly completed sets of MIPs have been identified from the completed genome sequence of organisms available at NCBI. The structural models of MIP proteins were created by defined protocol. The database aims to provide key information of MIPs in particular based on sequence as well as structures. This will further help to decipher the function of uncharacterized MIPs. For each MIP entry, this database contains information about the source, gene structure, sequence features, substitutions in the conserved NPA motifs, structural model, the residues forming the selectivity filter and channel radius profile. For selected set of MIPs, it is possible to derive structure-based sequence alignment and evolutionary relationship. Sequences and structures of selected MIPs can be downloaded from MIPModDB database. | major intrinsic protein, model, protein structure, structural model, sequence, structure, superfamily, genome sequence, amino acid sequence, motif, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Indian Institute of Technology Kanpur; Uttar Pradesh; India |
Government of India | PMID:22080560 | Free | nlx_151460, biotools:mipmoddb | https://bio.tools/mipmoddb | SCR_006058 | Major Intrinsic Protein superfamily Models, MIPModDB - Major Intrinsic Protein superfamily Models | 2026-02-14 02:06:25 | 6 | ||||
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ProOpDB Resource Report Resource Website 10+ mentions |
ProOpDB (RRID:SCR_006111) | ProOpDB | data or information resource, database | The Prokaryotic Operon DataBase (ProOpDB) constitutes one of the most precise and complete repository of operon predictions in our days. Using our novel and highly accurate operon algorithm, we have predicted the operon structures of more than 1,200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved including: i) organism name, ii) metabolic pathways, as defined by the KEGG database, iii) gene orthology, as defined by the COG database, iv) conserved protein motifs, as defined by the Pfam database, v) reference gene, vi) reference operon, among others. In order to limit the operon output to non-redundant organisms, ProOpDB offers an efficient protocol to select the more representative organisms based on a precompiled phylogenetic distances matrix. In addition, the ProOpDB operon predictions are used directly as the input data of our Gene Context Tool (GeConT) to visualize their genomic context and retrieve the sequence of their corresponding 5�� regulatory regions, as well as the nucleotide or amino acid sequences of their genes. The prediction algorithm The algorithm is a multilayer perceptron neural network (MLP) classifier, that used as input the intergenic distances of contiguous genes and the functional relationship scores of the STRING database between the different groups of orthologous proteins, as defined in the COG database. Nevertheless, the operon prediction of our method is not restricted to only those genes with a COG assignation, since we successfully defined new groups of orthologous genes and obtained, by extrapolation, a set of equivalent STRING-like scores based on conserved gene pairs on different genomes. Since the STRING functional relationships scores are determined in an un-bias manner and efficiently integrates a large amount of information coming from different sources and kind of evidences, the prediction made by our MLP are considerably less influenced by the bias imposed in the training procedure using one specific organism. | genome, operon, gene pair, gene, operon prediction, metabolic pathway, gene orthology, conserved protein motif, protein motif, reference gene, reference operon, visualization, regulatory region, nucleotide, amino acid, sequence, phylogeny, FASEB list |
is related to: COG is related to: KEGG is related to: Pfam has parent organization: National Autonomous University of Mexico; Mexico City; Mexico |
CONACyT 60127-Q; CONACyT SALUD-2007-C01-68992; DGAPA IN212708 |
PMID:20385580 | nlx_151585 | SCR_006111 | Prokaryotic Operon DataBase (ProOpDB), Prokaryotic Operon DataBase | 2026-02-14 02:05:54 | 35 | ||||||
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ProRepeat Resource Report Resource Website 1+ mentions |
ProRepeat (RRID:SCR_006113) | ProRepeat | data or information resource, database | ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats' corresponding codons. | amino acid, tandem, repeat, protein, sequence, nucleotide sequence, repeat fragment, protein repeat, proteome, sequence length, gene, taxon, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: UniProtKB is related to: RefSeq has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
PMID:22102581 | nlx_151587, biotools:prorepeat | https://bio.tools/prorepeat | SCR_006113 | 2026-02-14 02:05:59 | 1 | |||||||
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SILVA Resource Report Resource Website 10000+ mentions |
SILVA (RRID:SCR_006423) | data or information resource, database | High quality ribosomal RNA databases providing comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Supplementary services include a rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. Alignment tool, SINA, is available for download as well as available for use online. | ribosomal rna, gene sequence, gene, sequence, alignment, taxonomy, 16s, 18s, 23s, 28s, phylogeny, probe, primer, alignment service, fish, arb, ribocon, geoblast, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: RNAcentral is related to: ARB project is related to: SINA is related to: European ribosomal RNA database has parent organization: German Collection of Microorganisms and Cell Cultures |
German Collection of Microorganisms and Cell Cultures | PMID:23193283 PMID:24293649 PMID:17947321 |
biotools:silva, OMICS_01514, nif-0000-03464, r3d100011323, rid_000103 | https://bio.tools/silva https://doi.org/10.17616/R3FP60 |
SCR_006423 | SILVA rRNA database, SILVA - high quality ribosomal RNA databases | 2026-02-14 02:06:26 | 13429 | ||||||
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ViralZone Resource Report Resource Website 100+ mentions |
ViralZone (RRID:SCR_006563) | ViralZone | data or information resource, database | ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. ViralZone project is handled by the virus program of SwissProt group. Proteins popups were developed in collaboration with Prof. Christian von Mering and Andrea Franceschini, Bioinformatics Group , Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, funded in part by the SIB Swiss Institute of bioinformatics. All pictures in ViralZone are copyright of the SIB Swiss Institute of Bioinformatics. | dna virus, rna virus, virus, dna, rna, genomic, proteomic, sequence, reference strain, image, virion, retro-transcribing virus, genome, bibliographic, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Institute of Bioinformatics | PMID:20947564 | biotools:viralzone, r3d100013314, nlx_144372 | https://bio.tools/viralzone https://doi.org/10.17616/R31NJMRM |
http://www.expasy.org/viralzone/ | SCR_006563 | Viral Zone | 2026-02-14 02:06:34 | 128 | ||||
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Tetraodon nigroviridis Database Resource Report Resource Website |
Tetraodon nigroviridis Database (RRID:SCR_007123) | data or information resource, database | This database have been funded by the National Human Genome Research Institute (NHGRI) to produce shotgun sequence of the Tetraodon nigriviridis genome. The strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated. Whole genome shotgun libraries were prepared from Tetraodon genomic DNA obtained from the laboratory of Jean Weissenbach at Genoscope. Additional sequence data of approximately 2.5X coverage of Tetraodon has also been generated by Genoscope in plasmid and BAC end reads. Broad and Genoscope intend to pool their data and generate whole genome assemblies. Tetraodon nigroviridis is a freshwater pufferfish of the order Tetraodontiformes and lives in the rivers and estuaries of Indonesia, Malaysia and India. This species is 20-30 million years distant from Fugu rubripes, a marine pufferfish from the same family. The gene repertoire of T. nigroviridis is very similar to that of other vertebrates. However, its relatively small genome of 385 Mb is eight times more compact than that of human, mostly because intergenic and intronic sequences are reduced in size compared to other vertebrate genomes. These genome characteristics along with the large evolutionary distance between bony fish and mammals make Tetraodon a compact vertebrate reference genome - a powerful tool for comparative genetics and for quick and reliable identification of human genes. | estruary, evolutionary, fish, freshwater, fugu rubripes, gene, genetic, bac, bony, distance, dna, genome, genomic, human, intergenic, intronic, nigriviridis, plasmid, pufferfish, river, sequence, sequencing, shotgun, specie, tetraodon, tetraodontiformes, vertebrate | nif-0000-20998 | SCR_007123 | TND | 2026-02-14 02:05:58 | 0 |
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