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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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HCV Sequence Database Resource Report Resource Website 10+ mentions |
HCV Sequence Database (RRID:SCR_006019) | HCV Sequence Database | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. This central website provides annotated sequences and analysis tools that will be helpful to HCV scientists worldwide. Things you can do: * Find sequences in the database * Download sequences from the database * Retrieve data about the sequences * Analyze sequences * Work with the sequences using our tools * Download ready-made alignments The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses. | hepatitis c virus, sequence, annotation | has parent organization: HCV Databases | Hepatitis C | NIAID | PMID:15377502 | Public | nlx_151411 | SCR_006019 | Hepatitis C Sequence Database, Hepatitis C Virus Sequence Database, Los Alamos hepatitis C sequence database | 2026-07-28 09:41:30 | 19 | ||||
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PRED-GPCR Resource Report Resource Website 1+ mentions |
PRED-GPCR (RRID:SCR_006196) | PRED-GPCR | service resource, data set, data or information resource, data analysis service, production service resource, analysis service resource | A prediction tool for GPCR Family Classification from sequence alone based on a probabilistic method that uses family-specific profile Hidden Markov Models. The PRED-GPCR system is based on a probabilistic method that uses family specific profile HMMs in order to determine to which GPCR family a query sequence belongs or resembles. The approach proposed in this method exploits the descriptive power of profile HMMs along with an exhaustive discrimination assessment method to select only highly selective and sensitive profiles, for each family. The collection of these profiles constitutes a signature library, which is scanned, for significant matches with a given query sequence. The output report for a query sequence consists of two sections: * A ranked list of the profile HMM matches, below the selected individual motif E-value cutoff, along with their corresponding family. * A ranked list of the Combined P-values, E-values as well as the number of profiles matched for each family. To cross-evaluate your results you can browse through Swiss-Prot, Trembl, Pfam and Prosite family related entries. | g-protein coupled receptor, classification, hidden markov model, sequence, fasta, family classification, motif, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:15215415 | nlx_151741, biotools:pred-gpcr | https://bio.tools/pred-gpcr | SCR_006196 | PRED-GPCR: GPCRs Family classification from sequence alone | 2026-07-28 09:41:33 | 2 | ||||||
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Pseudomonas Genome Database Resource Report Resource Website 100+ mentions |
Pseudomonas Genome Database (RRID:SCR_006590) | PseudoCAP | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Database of peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome expanded to include all Pseudomonas species to facilitate cross-strain and cross-species genome comparisons with high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP (Pseudomonas aeruginosa Community Annotation Project) participating researchers. If you are interested in participating, you are invited to get involved. Many annotations, DNA sequences, Orthologs, Intergenic DNA, and Protein sequences are available for download. | gene, genome, annotation, localization, prokaryote, pseudomonas aeruginosa, sequence, subcellular, cystic fibrosis, ortholog, annotation, dna sequence, intergenic dna, protein sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: Debian is listed by: bio.tools is related to: AmiGO has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: University of British Columbia; British Columbia; Canada |
Cystic Fibrosis Foundation Therapeutics Inc | PMID:18978025 | nif-0000-03369, r3d100012086, biotools:pseudomonas_genome_database | https://bio.tools/pseudomonas_genome_database, https://doi.org/10.17616/R3935H | SCR_006590 | Pseudomonas Genome Database - Improving Disease Treatment Through Genome Research | 2026-07-28 09:41:37 | 489 | |||||
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Generate Pseudo-Random Numbers Resource Report Resource Website 1+ mentions |
Generate Pseudo-Random Numbers (RRID:SCR_006535) | data or information resource, topical portal, portal | This module implements pseudo-random number generators for various distributions. For integers, uniform selection from a range. For sequences, uniform selection of a random element, a function to generate a random permutation of a list in-place, and a function for random sampling without replacement. On the real line, there are functions to compute uniform, normal (Gaussian), lognormal, negative exponential, gamma, and beta distributions. For generating distributions of angles, the von Mises distribution is available. Sponsors: This resource is supported by ASTi logo Advanced Simulation Technology Inc. (ASTi); Array BioPharma Inc.; BizRate.com; Canonical Ltd.; CCP Games; cPacket Networks; EarnMyDegree.com; Enthought Inc.; Exoweb Ltd.; Google; HitMeister Inc.; IronPort Systems; KNMP; Lucasfilm; Madison Tyler LLC.; Merfin, LLC.; Microsoft; OpenEye Scientific Software; Opsware, Inc.; O''Reilly & Associates, Inc.; PropertySold.ca; Rogue Wave; SEO Moves; Strakt Holdings, Inc.; Sun Microsystems; Tabblo; ZeOmega, LLC., and Zope Corporation. | element, function, generator, computation, distribution, integer, lognormal, module, number, pseudo-random, range, sampling, sequence | nif-0000-30012 | http://docs.python.org/lib/module-random.html | SCR_006535 | Generate Pseudo | 2026-07-28 09:41:35 | 1 | |||||||||
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MaizeGDB Resource Report Resource Website 500+ mentions |
MaizeGDB (RRID:SCR_006600) | MaizeGDB | service resource, data or information resource, data repository, organism-related portal, data analysis service, storage service resource, database, production service resource, analysis service resource, topical portal, portal | Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images. | zea mays, corn, model organism, genome, locus, metabolic pathway, genetics, genomics, sequence, gene product, function, literature reference, phenotype, trait, pest, gel pattern, mutant, blast, gene, image, corn, genotype-environment interaction, gene mapping, plant genome mapping, plant genome, gold standard, bio.tools, FASEB list |
is listed by: re3data.org is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenBank has parent organization: University of Maryland; Maryland; USA works with: Maize Database of Images and Genomes |
USDA ; USDA/ARS ; NSF ; National Corn Growers Association |
PMID:21624896 PMID:18769488 PMID:15888678 PMID:14681441 |
Free, Freely available, Acknowledgement requested, The community can contribute to this resource | OMICS_01655, biotools:MaizeDIG, nif-0000-03096, r3d100010795 | https://bio.tools/MaizeDIG, https://doi.org/10.17616/R3V32B | SCR_006600 | Maize Genetics and Genomics Database, MaizeGDB, MaizeGDB Locus | 2026-07-28 09:41:37 | 806 | ||||
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Rat Genome Database (RGD) Resource Report Resource Website 100+ mentions |
Rat Genome Database (RGD) (RRID:SCR_006444) | RGD | service resource, data or information resource, data repository, database, storage service resource | Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources. | RIN, Resource Information Network, mouse, rat, human, gene, qtl, marker, map, strain, sequence, est, genome, ontology, pathway, comparative genomics, physiology, phenotype, disease, model organism, proteomics, function, genetic, genomic, variation, immunology, behavior, knockout, inbred rat strain, mutant, congenic rat, recombinant inbred rat, data analysis service, organism supplier, genotype, gold standard, FASEB list, RRID Community Authority |
uses: InterMOD is used by: ChannelPedia is used by: Resource Identification Portal is used by: DisGeNET is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal is listed by: re3data.org is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: Rat Gene Symbol Tracker is related to: MPO is related to: NIF Data Federation is related to: MONARCH Initiative is related to: Vertebrate Trait Ontology is related to: Biositemaps is related to: One Mind Biospecimen Bank Listing is related to: AmiGO is related to: OMICtools is related to: re3data.org is related to: Integrated Manually Extracted Annotation is related to: OntoMate has parent organization: Medical College of Wisconsin; Wisconsin; USA is parent organization of: Diabetes Disease Portal is parent organization of: Rat Strain Ontology is parent organization of: Rat Strain Ontology is parent organization of: Renal Disease Portal is organization facet of: Alliance of Genome Resources |
NHLBI | PMID:23434633 PMID:18996890 PMID:17151068 |
Free, Freely available | nif-0000-00134, r3d100010417, OMICS_01660 | https://doi.org/10.17616/R3WK60 | SCR_006444 | , Rat Genome Database, RGD | 2026-07-28 09:41:35 | 272 | ||||
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FlyBase Resource Report Resource Website 1000+ mentions |
FlyBase (RRID:SCR_006549) | FB | service resource, data or information resource, data repository, organism-related portal, database, storage service resource, topical portal, portal | Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar. | RIN, Resource Information Network, mutant, gene, genome, blast, genotype, phenotype, allele, sequence, stock, image, movie, controlled term, video resource, image collection, life-cycle, genome, expression, rna-seq, genetics, drosophilidae, bio.tools, FASEB list, RRID Community Authority |
is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is used by: Drososhare is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: Resource Information Network is related to: FlyMine is related to: Virtual Fly Brain is related to: AmiGO is related to: Drosophila melanogaster Exon Database is related to: HomoloGene is related to: UniParc at the EBI is related to: UniParc is related to: Gene Ontology is related to: NIH Data Sharing Repositories is related to: GBrowse is related to: Integrated Manually Extracted Annotation is related to: PhenoGO has parent organization: Harvard University; Cambridge; United States has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: Indiana University; Indiana; USA has parent organization: University of New Mexico; New Mexico; USA is parent organization of: Drosophila anatomy and development ontologies is parent organization of: Fly Taxonomy is parent organization of: FlyBase Controlled Vocabulary is parent organization of: Drosophila Development Ontology is organization facet of: Alliance of Genome Resources |
MRC ; Indiana Genomics Initiative ; NSF ; NIH Blueprint for Neuroscience Research ; NIHGRI P41 HG000739 |
PMID:24234449 PMID:22127867 PMID:18948289 PMID:18641940 PMID:18160408 PMID:17099233 PMID:16381917 PMID:15608223 PMID:12519974 PMID:11752267 PMID:11465064 PMID:9847148 PMID:9399806 PMID:9045212 PMID:8594600 PMID:8578603 PMID:7937045 PMID:7925011 |
nif-0000-00558, r3d100010591, OMICS_01649, biotools:flybase | https://bio.tools/flybase, https://doi.org/10.17616/R3903Q | http://flybase.net | SCR_006549 | flybase A Drosophila Genomic and Genetic Database, FlyBase: A Database of Drosophila Genes and Genomes, FLYBASE, FlyBase: A Database of Drosophila Genes & Genomes, FB | 2026-07-28 09:41:35 | 4025 | ||||
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Decombinator Resource Report Resource Website 10+ mentions |
Decombinator (RRID:SCR_006732) | software application, data analysis software, software resource, data processing software, software toolkit | Software suite for analysis of T cell receptor repertoire data. Used for fast, efficient analysis of T cell receptor (TcR) repertoire samples, designed to be accessible to those with no previous programming experience. | Python, t-cell receptor sequence, t-cell receptor, sequence, deep sequencing, TCR repertoires, repertoire data, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University College London; London; United Kingdom |
PMID:23303508 PMID:32853330 |
Free, Available for download, Freely available | biotools:decombinator, OMICS_00001 | https://github.com/innate2adaptive/Decombinator, https://bio.tools/decombinator | SCR_006732 | Decombinator v2.2, Decombinator v4.0.3 | 2026-07-28 09:41:39 | 28 | ||||||
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1000 Genomes: A Deep Catalog of Human Genetic Variation Resource Report Resource Website 5000+ mentions |
1000 Genomes: A Deep Catalog of Human Genetic Variation (RRID:SCR_006828) | 1000 Genomes | data set, data or information resource, organization portal, database, consortium, portal | International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes | genetic variation, gene, next-generation sequencing, sequence, alignment, genome, single-nucleotide polymorphism, structural variant, haplotype, genome-wide association study, pharmacology, genetics, biomarker, consortium, data sharing, genotype, phenotype, FASEB list |
uses: NHGRI Sample Repository for Human Genetic Research is used by: BioSample Database at EBI is listed by: OMICtools is listed by: re3data.org is listed by: Consortia-pedia is related to: MOSAIK is related to: ART is related to: SNAP - SNP Annotation and Proxy Search has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: Harvard Medical School; Massachusetts; USA has parent organization: Broad Institute has parent organization: NCBI has parent organization: European Bioinformatics Institute has parent organization: National Human Genome Research Institute |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom ; Beijing Genomics Institute; Shenzhen; China ; NHGRI ; 454 Life Sciences Roche ; Life Technologies ; Illumina |
Free, Public, Restrictions apply, Http://www.1000genomes.org/data#DataAccess | r3d100010180, nlx_143819, OMICS_00261 | https://doi.org/10.17616/R3CP4M | SCR_006828 | International 1000 Genomes Project, 1000 Genomes Project | 2026-07-28 09:41:40 | 5486 | |||||
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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 | 2026-07-28 09:41:18 | 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 | 2026-07-28 09:41:20 | 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 | 2026-07-28 09:41:18 | 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 | 2026-07-28 09:41:32 | 6 | ||||
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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 | 2026-07-28 09:41:27 | 1 | |||||||
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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 | 2026-07-28 09:41:31 | 35 | ||||||
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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 | 2026-07-28 09:41:35 | 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 | 2026-07-28 09:41:37 | 128 | ||||
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Yeast Intron Database Resource Report Resource Website 1+ mentions |
Yeast Intron Database (RRID:SCR_007144) | Yeast Intron Database | data or information resource, database | Database of information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Listed are known spliceosomal introns in the yeast genome and the splice sites actually used are documented. Through the use of microarrays designed to monitor splicing, they are beginning to identify and analyze splice site context in terms of the nature and activities of the trans-acting factors that mediate splice site recognition. In version 3.0, expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors is included. These data are displayed on each intron page for browsing and can be downloaded for other types of analysis. | intron, spliceosomal, splicing, genome, intron splice signal, sequence, splice site |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
W. M. Keck Foundation ; Packard Foundation ; NIH |
PMID:11988574 | The community can contribute to this resource | nif-0000-03649, OMICS_01890 | http://www.cse.ucsc.edu/research/compbio/yeast_introns.html | SCR_007144 | Ares lab Yeast Intron Database | 2026-07-28 09:41:42 | 2 | ||||
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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 | 2026-07-28 09:41:44 | 0 | ||||||||||
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rSeq Resource Report Resource Website 1+ mentions |
rSeq (RRID:SCR_000562) | software toolkit, source code, software resource | A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations. | rna, sequence, read quality assessment, reference sequence generation, sequence mapping, gene, isoform expressions estimations, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
Free, Available for download, Freely available, | OMICS_01288, biotools:rseq | https://bio.tools/rseq | SCR_000562 | RNA-Seq Analyzer, rSeq: RNA-Seq Analyzer | 2026-07-28 09:40:02 | 4 |
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