Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains Resource Report Resource Website |
Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains (RRID:SCR_002831) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. LOC3d is a database of predicted subcellular localization for eukaryotic proteins of known 3-D structure taken from the Protein Databank. Subcellular localization is currently predicted using four different methods: predictNLS (nuclear localization signal), LOChom (using homology), LOCkey (using keywords) and LOC3d (neural network based prediction). The reported localization is based on the method which predicts localization of a given protein with the highest confidence. LOCtree is a novel system of support vector machines (SVMs) that predict the subcellular localization of proteins, and DNA-binding propensity for nuclear proteins, by incorporating a hierarchical ontology of localization classes modeled onto biological processing pathways. Biological similarities are incorporated from the description of cellular components provided by the gene ontology consortium (GO). GO definitions have been simplified and tailored to the problem of protein sorting. Technically the ontology has been implemented using a decision tree with SVMs as the nodes. LOCtree, was extremely successful at learning evolutionary similarities among subcellular localization classes and was significantly more accurate than other traditional networks at predicting subcellular localization. Whenever available, LOCtree also reports predictions based on the following: 1) Nuclear localization signals found by PredictNLS, 2) Localization inferred using Prosite motifs and Pfam domains found in the protein, and 3) SWISS-PROT keywords associated with a protein. Localization is inferred in the last two cases using the entropy-based LOCkey algorithm. Additional information can be found in the LOCtree manuscript and associated PredictNLS and LOCkey publications. | eukaryotic, gene, binding, biological, dna, localization, nuclear, pathway, protein, structure, subcellular, vector, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
PMID:12824321 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25200, biotools:loc3d | https://bio.tools/loc3d | SCR_002831 | LOC3d | 2026-08-06 09:25:44 | 0 | ||||||
|
ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters Resource Report Resource Website 1+ mentions |
ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters (RRID:SCR_002276) | ABS | database, data or information resource | Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available. | gene, alignment, annotation, binding, computational, genome, nucleotide, ortholog, prediction, promoter, sequence, target, transcription, transcriptional factor, binding site, promoter sequence, protein motif, benchmark, transcription factor binding site, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IntegromeDB has parent organization: Center for Genomic Regulation; Barcelona; Spain |
European Union FP6 contract LSHG-CT-2003-503265 | PMID:16381947 | Acknowledgement requested, GNU General Public License, v2 | biotools:alggen, nif-0000-21006 | https://bio.tools/alggen | SCR_002276 | A database of Annotated regulatory Binding Sites from orthologous promoters | 2026-08-06 09:25:38 | 1 | ||||
|
T3DB Resource Report Resource Website 10+ mentions |
T3DB (RRID:SCR_002672) | T3DB | database, data or information resource | Database that combines detailed toxin data with comprehensive toxin target information. The database currently houses 3,053 toxins described by 32,276 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to 1,670 corresponding toxin target records. Altogether there are 37,084 toxin, toxin target associations. (March 2014) Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5,454 sources sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches | toxicology, toxin, pollutant, pesticide, drug, food, gene-drug, interaction, gene, phenotype, mechanism, bio.tools |
is used by: NIF Data Federation is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: FMA has parent organization: University of Alberta; Alberta; Canada |
Alberta Advanced Education and Technology ; Canadian Institutes of Health Research ; Genome Alberta ; Genome Canada |
PMID:19897546 | Free, Available for download, Freely available | r3d100012189, nif-0000-22933, biotools:t3db, OMICS_01592 | https://bio.tools/t3db, https://doi.org/10.17616/R3VM0R | SCR_002672 | Toxin-Target Database, Toxin Toxin-Target Database, Toxin and Toxin Target Database, Toxin, Toxin Toxin Target Database | 2026-08-06 09:25:41 | 24 | ||||
|
HINT Resource Report Resource Website 100+ mentions |
HINT (RRID:SCR_002762) | HINT | database, data or information resource | A database of high-quality protein-protein interactions in different organisms. | protein-protein interaction, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Cornell University; New York; USA |
PMID:22846459 | Free, Freely available, Available for download | OMICS_02898, biotools:hint | https://bio.tools/hint | SCR_002762 | High-quality INTeractomes | 2026-08-06 09:25:42 | 306 | |||||
|
Entrez Gene Resource Report Resource Website 1000+ mentions |
Entrez Gene (RRID:SCR_002473) | NCBI_Gene, NCBI Genen NCBI Entrez | database, data or information resource | Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available. | gene, gene expression, gene location, gene map, gene prediction, genome, genome sequence analysis, phenotype, nomenclature, gene mapping, protein, genetic code, function, annotation, gold standard, bio.tools |
is used by: Animal QTLdb is used by: NIF Data Federation is used by: LIPID MAPS Proteome Database is used by: DisGeNET is used by: Nowomics is used by: Cytokine Registry is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Vesiclepedia is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Rat Gene Symbol Tracker is related to: Gene Reference into Function is related to: Integrated Molecular Interaction Database is related to: Biomine is related to: SEGS is related to: STOP is related to: Coremine Medical is related to: Consensus CDS is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: Array Information Library Universal Navigator is related to: biomaRt has parent organization: NCBI works with: Open Regulatory Annotation Database |
PMID:17148475 PMID:21115458 |
Free, Freely available | nif-0000-02801, biotools:entrez_gene, OMICS_01651, r3d100010650 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene, https://bio.tools/entrez_gene, https://doi.org/10.17616/R3603S | SCR_002473 | NCBI Gene, Gene - Gene mapped phenotypes, Gene - Gene and mapped phenotypes, Gene Database, GeneID | 2026-08-06 09:25:40 | 2830 | |||||
|
DBTSS: Database of Transcriptional Start Sites Resource Report Resource Website 100+ mentions |
DBTSS: Database of Transcriptional Start Sites (RRID:SCR_002354) | DBTSS | database, data or information resource | Database of transcriptional start sites (TSSs) representing exact positions in the genome based on a unique experimentally validated TSS sequencing method, TSS Seq. A major part of human adult and embryonic tissues are covered. DBTSS contains 491 million TSS tag sequences collected from a total of 20 tissues and 7 cell cultures. Also integrated is generated RNA-seq data of subcellular- fractionated RNAs and ChIP Seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. Also included is external epigenomic data, such as chromatin map of the ENCODE project. They associated those TSS information with public and original SNV data, in order to identify single nucleotide variations (SNVs) in the regulatory regions. | cdna, cdna library, transcriptional start site, transcriptome, transcriptome analysis, tss-seq, genome, adult human, embryonic, cell, rna-seq, subcellular, rna, chip seq data, histone modification, rna polymerase ii, transcriptional regulatory factor, cell line, single nucleotide variation, regulatory region, genetic valuation, transcriptional regulation, bio.tools, FASEB list |
is used by: Transcriptional Regulatory Element Database is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:22086958 PMID:19910371 PMID:17942421 PMID:16381981 PMID:14681363 PMID:11752328 |
nif-0000-02738, biotools:dbtss, OMICS_01860 | https://bio.tools/dbtss | SCR_002354 | DBTSS: Database of Transcriptional Start Sites, DataBase of Transcriptional Start Sites | 2026-08-06 09:25:38 | 124 | |||||
|
RESID Resource Report Resource Website 10+ mentions |
RESID (RRID:SCR_003505) | RESID | database, data or information resource | A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. It provides: systematic and alternate names, atomic formulas and masses, enzyme activities generating the modifications, keywords, literature citations, Gene Ontology cross-references, Protein Information Resource (PIR) and SWISS-PROT protein sequence database feature table annotations, structure diagrams and molecular models. Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries. | protein cross-link, protein modification, protein structure, protein, structure, annotation, amino-terminal, carboxyl-terminal, peptide chain cross-link, post-translational modification, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:15174122 PMID:12520062 |
nif-0000-03400, r3d100000023, biotools:resid | https://bio.tools/resid, https://doi.org/10.17616/R3Z59M | http://www.ebi.ac.uk/RESID/ | SCR_003505 | RESID Database at the EBI, RESID Database at PIR, RESID Database of Protein Modifications, RESID Database | 2026-08-06 09:25:55 | 10 | |||||
|
GeneFisher Resource Report Resource Website 10+ mentions |
GeneFisher (RRID:SCR_003060) | GeneFisher, GeneFisher2 | data analysis service, production service resource, analysis service resource, service resource | A web-based program for designing degenerate primers. The procedure leads to isolation of genes in a target organism using multiple alignments of related genes from different organisms. The term gene fishing refers to the technique where PCR is used to isolate a postulated but unknown target sequence from a pool of DNA. | primer design, gene, degenerate primer, degenerate, primer, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:8877506 | Free, Freely available | biotools:genefisher, OMICS_02341 | https://bio.tools/genefisher | SCR_003060 | GeneFisher2 - Interactive PCR Primer Design | 2026-08-06 09:25:47 | 37 | |||||
|
IPI Resource Report Resource Website 50+ mentions |
IPI (RRID:SCR_003012) | IPI | database, data or information resource | IPI provides a top level guide to the main databases (UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, RefSeq, Ensembl, TAIR, H-InvDB, Vega) that describe the proteomes of higher eukaryotic organisms. IPI: :1. effectively maintains a database of cross references between the primary data sources :2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) :3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. As previously announced, the closure of IPI has been proposed for some time. Replacement data sets are now available through UniProt for human and mouse; sets for the other species contained within IPI are expected to be included as part of the UniProt release 2011_07. To allow users time to transition to using the new UniProt data sets, IPI releases will continue to be produced throughout the summer. The final release will be made in September 2011. Thereafter, the IPI website will cease to be maintained, although previous releases of the dataset will continue to be available from the FTP site. We would like to thank our users for their support and interest in this service. | human, mouse, rat, zebrafish, arabidopsis, chicken, cow, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: UniProt DAS has parent organization: European Bioinformatics Institute works with: PremierBiosoft Proteo IQ Software |
PMID:15221759 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ipi, nif-0000-03043 | https://bio.tools/ipi | SCR_003012 | International Protein Index, IPI - International Protein Index | 2026-08-06 09:25:46 | 76 | |||||
|
IPD - Immuno Polymorphism Database Resource Report Resource Website 10+ mentions |
IPD - Immuno Polymorphism Database (RRID:SCR_003004) | IPD | database, data or information resource | A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines. | polymorphic gene, immune system, gene, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
European Union contract QLRI-CT-200!-01325; NCI P01 111412 |
PMID:19875415 PMID:18449992 PMID:15608253 |
biotools:ipd, nif-0000-03038, r3d100010797 | https://bio.tools/ipd, https://doi.org/10.17616/R3KK7K | SCR_003004 | IPD-The Immuno Polymorphism Database, IPD - The Immuno Polymorphism Database | 2026-08-06 09:25:46 | 24 | |||||
|
eMouseAtlas Resource Report Resource Website 50+ mentions |
eMouseAtlas (RRID:SCR_002981) | EMAP, EMA, EMAGE, MAP, EMAP, MAP2.0, | database, data or information resource, atlas | Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped. | Mouse Atlas Project, molecular neuroanatomy resource, adult mouse, mouse, brain, c57bl/6j, magnetic resonance microscopy, diffusion-weighted image, blockface imaging, immunohistochemistry, in situ hybridization, neuroanatomy, mri, dti, brain architecture, gene expression, neuroimaging, ontology, connectivity, histology, neuronal tract tracing, genetic labeling, newborn mouse, experimental protocol, bio.tools, ontology, histology, mouse embryo, gene expression, gxd query interface, digital anatomical atlas, spatial region, domain, 2d, 3d, virtual embryo model, development atlas, standard anatomical nomenclature, developmental staging criteria, spatially mapped, anatomy nomenclature, molecular neuroanatomy resource, embryonic mouse, FASEB list |
is related to: GUDMAP Ontology is related to: EMAGE Gene Expression Database is related to: EMAGE Gene Expression Database is related to: HUDSEN is related to: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project has parent organization: University of Edinburgh; Scotland; United Kingdom has parent organization: Jackson Laboratory is parent organization of: Minimal Anatomical Terminology |
Medical Research Council ; NINDS ; NIBIB ; NIDA ; NIDCD ; NIA |
PMID:15043218 PMID:18077470 PMID:16381949 |
Free, Freely available | nif-0000-00038, nif-0000-00505, biotools:emap, biotools:ma, SCR_007281 | http://www.emouseatlas.org/emap/home.html, https://bio.tools/emap, https://bio.tools/ma | http://genex.hgu.mrc.ac.uk/, http://www.loni.ucla.edu/MAP/ | SCR_002981 | emouseatlas, e-mouse Atlas, EMAGE Gene Expression Database, EMA, Edinburgh Mouse Atlas of Gene Expression, e-Mouse Atlas, EMA Anatomy Atlas of Mouse Development | 2026-08-06 09:25:46 | 69 | |||
|
ResponseNet Resource Report Resource Website 1+ mentions |
ResponseNet (RRID:SCR_003176) | ResponseNet | data analysis service, production service resource, analysis service resource, service resource | WebServer that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins and genes, such as a set of disease-associated proteins and a set of differentially expressed disease genes, and a molecular interaction network (i.e., interactome). The output is a sparse, high-probability interactome sub-network connecting the two sets that is biased toward signaling pathways. This sub-network exposes additional proteins that are potentially involved in the studied condition and their likely modes of action. Computationally, it is formulated as a minimum-cost flow optimization problem that is solved using linear programming. | interactome, gene, protein, signaling pathway, signaling, regulatory, pathway, regulatory pathway, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel |
PMID:23761447 PMID:21576238 |
Free, Freely available | biotools:responsenet, OMICS_01562 | https://bio.tools/responsenet | http://netbio.bgu.ac.il/respnet/ | SCR_003176 | 2026-08-06 09:25:49 | 4 | |||||
|
IntEnz- Integrated relational Enzyme database Resource Report Resource Website 10+ mentions |
IntEnz- Integrated relational Enzyme database (RRID:SCR_002992) | IntEnz | database, data or information resource | IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. | enzyme categories, enzyme classification, enzyme nomenclature, enzyme reaction categories, enzyme, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: ENZYME has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics |
European Union SLING 226073 | PMID:14681451 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03028, biotools:intenz, r3d100010803 | https://bio.tools/intenz | SCR_002992 | 2026-08-06 09:25:46 | 13 | |||||
|
vcflib Resource Report Resource Website 100+ mentions |
vcflib (RRID:SCR_001231) | vcflib | software library, software toolkit, software resource | A C++ library for parsing and manipulating Variant Call Format (VCF) files, and many command-line utilities. The API provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users. | c++, sequence variation, genomic variation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:vcflib, OMICS_02112 | https://bio.tools/vcflib, https://sources.debian.org/src/libvcflib-dev/ | https://sources.debian.org/src/libvcflib-dev/ | SCR_001231 | 2026-08-06 09:25:21 | 119 | ||||||
|
CSDeconv Resource Report Resource Website |
CSDeconv (RRID:SCR_000016) | CSDeconv | data analysis software, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach. | sequence analysis software, transcription factor binding site, chip-seq, blind deconvolution, transcription binding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Rutgers University; New Jersey; USA has parent organization: University of South Australia; Adelaide; Australia |
PMID:20028542 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00436, biotools:csdeconv | https://bio.tools/csdeconv | SCR_000016 | 2026-08-06 09:25:06 | 0 | ||||||
|
fastqz Resource Report Resource Website |
fastqz (RRID:SCR_001006) | data management software, source code, software application, software resource | Source code used to compress FASTQ files. FASTQ is DNA sequencing machine output. | compress, source code, fastq output, fastq dna, fastq sequencing, fastq compress, fastq compressor, fastq files, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23533605 | Free, Available for download, Freely available | OMICS_00956, biotools:fastqz | https://bio.tools/fastqz | SCR_001006 | 2026-08-06 09:25:19 | 0 | |||||||
|
SeqEM Resource Report Resource Website 1+ mentions |
SeqEM (RRID:SCR_002021) | sequence analysis software, software resource, algorithm resource, data analysis software, data processing software, web application, software application | Online tool for utilizing a genotype calling algorithm for next-generation sequence data. | genotype, algorithm, sequence, rna, dna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Miami Miller School of Medicine; Florida; USA |
PMID:20861027 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00074, biotools:seqem | https://bio.tools/seqem | SCR_002021 | 2026-08-06 09:25:35 | 1 | |||||||
|
BeetleBase Resource Report Resource Website 50+ mentions |
BeetleBase (RRID:SCR_001955) | BEETLEBASE | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded. | red flour beetle, tribolium castaneum, sequence data, gene, mutant, genetic marker, expressed sequence tag, genome, blast, model organism, insect, developmental biology, genomics, genetics, entomology, development, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: RefSeq has parent organization: Kansas State University; Kansas; USA |
NCRR P20 RR16475 | PMID:18362917 PMID:17090595 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02599, biotools:beetlebase, r3d100010921 | https://bio.tools/beetlebase, https://doi.org/10.17616/R3G61K | http://bioinformatics.k-state.edu/BeetleBase/, http://www.bioinformatics.ksu.edu/BeetleBase/ | SCR_001955 | 2026-08-06 09:25:34 | 82 | ||||
|
SGA Resource Report Resource Website 10+ mentions |
SGA (RRID:SCR_001982) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software package that functions as a de novo genome assembler based on the concept of string graphs. It is designed as a modular set of programs used to assemble large genomes from high coverage short read data. | string, graph assembler, de novo assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
DOI:10.1101/gr.126953.111 | Free, Available for download, Freely available | OMICS_00028, biotools:sga | https://bio.tools/sga, https://sources.debian.org/src/sga/ | SCR_001982 | String Graph Assembler (SGA), String Graph Assembler | 2026-08-06 09:25:34 | 18 | ||||||
|
GSNAP Resource Report Resource Website 500+ mentions |
GSNAP (RRID:SCR_005483) | GSNAP | software resource, image analysis software, alignment software, data processing software, software application | Software to align single and paired end reads as short as 14 nt and of arbitrarily long length. Can detect short and long distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or database of known splice sites. Permits SNP-tolerant alignment to reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for study of methylation state. | next-generation sequencing, bio.tools, FASEB list |
is used by: Gsnap2Augustus is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20147302 | OMICS_00665, biotools:gsnap | https://bio.tools/gsnap | SCR_005483 | Genomic Short-read Nucleotide Alignment Program | 2026-08-06 09:26:21 | 784 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
