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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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