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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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My Cancer Genome Resource Report Resource Website 50+ mentions |
My Cancer Genome (RRID:SCR_004140) | MCG | database, data or information resource | A freely available online personalized cancer medicine knowledge resource for physicians, patients, caregivers and researchers that gives up-to-date information on what mutations make cancers grow and related therapeutic implications, including available clinical trials. It is a one-stop tool that matches tumor mutations to therapies, making information accessible and convenient for busy clinicians. | genome, disease, genome, medicine, clinical trial, mutation, therapy, FASEB list |
is listed by: OMICtools has parent organization: Vanderbilt University; Tennessee; USA |
Cancer, Tumor | PMID:32483629 | OMICS_01552 | SCR_004140 | MyCancerGenome.org | 2026-08-04 09:41:04 | 97 | ||||||
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JCVI GenProp Resource Report Resource Website 1+ mentions |
JCVI GenProp (RRID:SCR_004592) | JCVI GenProp | database, data or information resource, service resource | The Genome Properties system consists of a suite of Properties which are carefully defined attributes of prokaryotic organisms whose status can be described by numerical values or controlled vocabulary terms for individual completely sequenced genomes. The system has been designed to capture the widest possible range of attributes and currently encompasses taxonomic terms, genometric calculations, metabolic pathways, systems of interacting macromolecular components and quantitative and descriptive experimental observations (phenotypes) from the literature. You may search the Genome Properties Database in 1 of 3 ways: * Search For Predicted Properties in the CMR: The Genome Property Search allows you to search the Genome Property database for state information for selected genomes and properties. * Perform a Keyword Search for a Specific Property: Lists all Genome Properties that match a specific text string. You can choose to search All Fields within a genome property or the Property Name. * Browse Top Level Genome Properties: Click on the properties to see the specific genome property report page. The Genome Properties system presents key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties. | prokaryote, genome, genomics, a | has parent organization: JCVI CMR | NSF DBI-0110270; DOE DE-FG02-01ER63203 |
PMID:15347579 | nlx_58176 | http://www.tigr.org/Genome_Properties | SCR_004592 | Genome Properties, Genome Properties Database, JCVI CMR Genome Properties | 2026-08-04 09:41:10 | 1 | |||||
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Pain Genes database Resource Report Resource Website 10+ mentions |
Pain Genes database (RRID:SCR_004771) | PainGenesdb | database, data or information resource | Database of genes regulated by pain derived from published manuscripts describing results of pain-relevant knockout studies. The database has two levels of exploration: across-gene and within-gene. The across-gene level, the PainGenesdbSelector, is encountered first. All genes in the database can be accessed and sorted by their gene name, protein name, common names and acronyms, or genomic position (by navigating a graphic representation of the mouse genome). The gene and protein names can be selected from an alphabetical list, or by typing a text string into a search box. | knock out mouse, pain sensation, mice, mutant, knockout, gene, genome, protein | has parent organization: McGill University; Montreal; Canada | Pain | Louise Edwards Foundation | PMID:17574758 | nlx_77039, r3d100012129 | https://doi.org/10.17616/R3WP95 | SCR_004771 | PainGenes DB | 2026-08-04 09:41:12 | 15 | ||||
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NBC Resource Report Resource Website 1+ mentions |
NBC (RRID:SCR_004772) | NBC | data analysis service, analysis service resource, production service resource, service resource | Webserver for taxonomic classification of metagenomic reads. | metagenome, genome, virus, taxonomy, next-generation sequencing, taxonomic classification, classification |
is listed by: OMICtools has parent organization: Drexel University; Pennsylvania; USA |
NSF DBI-0845827; DOE DE-SC0004335 |
PMID:1062764 PMID:19956701 |
OMICS_01458 | SCR_004772 | Naive Bayes Classification tool, Na����ve Bayesian Classification tool, Naive Bayesian Classification Tool | 2026-08-04 09:41:12 | 3 | ||||||
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NCBI BioProject Resource Report Resource Website 10000+ mentions |
NCBI BioProject (RRID:SCR_004801) | database, data or information resource | Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP. | genome sequencing, sequencing, genotype, phenotype, sequence variant, epigenetic, data set, genome, assembly, annotation, mapping, cellular organism, gene mapping, gene expression, biological tag, gene rearrangement, genetic algorithm, genetic code, genetic genealogy, gold standard, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC has parent organization: NCBI |
NLM | PMID:22139929 | Free, Freely available | r3d100013330, nlx_143909, biotools:bioproject | http://www.ncbi.nlm.nih.gov/genomeprj, https://bio.tools/bioproject, https://doi.org/10.17616/R31NJMS2 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj | SCR_004801 | NCBI BioProject Database, BioProject | 2026-08-04 09:41:13 | 13968 | ||||
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ChIPBase Resource Report Resource Website 100+ mentions |
ChIPBase (RRID:SCR_005404) | ChIPBase | database, data or information resource | A database for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs (snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase currently includes millions of transcription factor binding sites (TFBSs) among 6 species. ChIPBase provides several web-based tools and browsers to explore TF-lncRNA, TF-miRNA, TF-mRNA, TF-ncRNA and TF-miRNA-mRNA regulatory networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chip-seq, gene, rna, microrna, long non-coding rna, non-coding, transcription factor binding site, protein, transcriptional regulation, annotation, regulatory element, transcription factor, genome, network, FASEB list |
is listed by: OMICtools has parent organization: Sun Yat-sen University; Guangdong; China |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00527 | SCR_005404 | 2026-08-04 09:41:22 | 145 | ||||||||
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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 | database, data or information resource | 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 | 2026-08-04 09:41:20 | 0 | |||||||
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AVIA Resource Report Resource Website 1+ mentions |
AVIA (RRID:SCR_005172) | AVIA | data analysis service, analysis service resource, production service resource, service resource | An interactive web-based tool to explore and interpret large sets of genomic variations (single nucleotide variations and insertion/deletions) to help guide and summarize genomic experiments. The tool is based on coupling a comprehensive annotation pipeline with a flexible visualization method. They leveraged the ANNOVAR (Wang et. al, 2010) framework for assigning functional impact to genomic variations by extending its list of reference annotation databases (RefSeq, UCSC, SIFT, Polyphen etc.) with additional in-house developed sources (Non-B DB, PolyBrowse). Further, because many users also have their own annotation sources, they have added the ability to supply their own files as well. The results can be obtained in tabular format or as tracks in whole genome circular views generated by the Circos application (Krzywinski et. al, 2009). Users can also select different sets of pre-computed tracks, including whole genome distributions of different genomic features (genes, exons, repeats), as well as variations analysis tracks for the 69 CGI public genomes for reference. | genomic variation, single nucleotide variation, insertion, deletion, indel, genome, annotation, visualization, impact analysis, mirna snp, mirna, snp, subtractive analysis, protein coding |
is listed by: OMICtools has parent organization: Frederick National Laboratory for Cancer Research has parent organization: NCI-Frederick |
PMID:24215028 | Acknowledgement requested | OMICS_00168 | SCR_005172 | Annotation Visualization and Impact Analysis | 2026-08-04 09:41:18 | 9 | ||||||
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Oncotator Resource Report Resource Website 100+ mentions |
Oncotator (RRID:SCR_005183) | Oncotator | data analysis service, analysis service resource, production service resource, service resource | A tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. Genomic Annotations, Protein Annotations, and Cancer Annotations are aggregated from many resources. A standalone version of Oncotator is being developed. | annotate, genomic, point mutation, indel, mutation, genome, protein, variant |
is listed by: OMICtools has parent organization: Broad Institute |
Cancer | OMICS_00178 | SCR_005183 | 2026-08-04 09:41:18 | 215 | ||||||||
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WEGO - Web Gene Ontology Annotation Plot Resource Report Resource Website 100+ mentions |
WEGO - Web Gene Ontology Annotation Plot (RRID:SCR_005827) | WEGO | data analysis service, analysis service resource, production service resource, service resource | Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool | visualization, gene ontology, gene, annotation, comparative genomics, histogram, directed acyclic graph, genomics, genome, ontology or annotation visualization, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: BGI; Shenzhen; China |
Zhejiang University ; Chinese Academy of Sciences ; Danish Basic Research Foundation ; Ministry of Science and Technology 2002AA104250; Ministry of Science and Technology CNGI-04-15-7A; National Natural Science Foundation of China 30399120; National Natural Science Foundation of China 90208019; National Natural Science Foundation of China 30200163; National Natural Science Foundation of China 90403130 |
PMID:16845012 | Free for academic use | biotools:wego, nlx_149334 | https://bio.tools/wego | SCR_005827 | BGI WEGO - Web Gene Ontology Annotation Plotting, Web Gene Ontology Annotation Plot | 2026-08-04 09:41:26 | 386 | ||||
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Transcriptional Regulatory Element Database Resource Report Resource Website 50+ mentions |
Transcriptional Regulatory Element Database (RRID:SCR_005661) | TRED | database, data or information resource | Collects mammalian cis- and trans-regulatory elements together with experimental evidence. Regulatory elements were mapped on to assembled genomes. Resource for gene regulation and function studies. Users can retrieve primers, search TF target genes, retrieve TF motifs, search Gene Regulatory Networks and orthologs, and make use of sequence analysis tools. Uses databases such as Genbank, EPD and DBTSS, and employ promoter finding program FirstEF combined with mRNA/EST information and cross-species comparisons. Manually curated. | Mammalian, cis, trans, regulatory, element, mapped, genome, gene, regulation, function, data, FASEB list |
uses: GenBank uses: Eukaryotic Promoter Database uses: DBTSS: Database of Transcriptional Start Sites has parent organization: Cold Spring Harbor Laboratory |
NCI ; NHGRI HG001696 |
PMID:17202159 | Free, Freely available | nif-0000-03585 | SCR_005661 | Transcriptional Regulatory Element Database | 2026-08-04 09:41:24 | 78 | |||||
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Tractor db Resource Report Resource Website 1+ mentions |
Tractor db (RRID:SCR_005610) | Tractor db | database, data or information resource | Database of computationally predicted Transcription Factors and binding sites in gamma-proteobacterial genomes. The user may browse a map containing all known E. coli transcription factors and regulatory interactions that connect them, and retrieve information on the conservation of each regulatory interaction across the 30 organisms included in the database. Downloading the information is straightforward, and navigation tabs added to dynamic pages ease navigation between the five interfaces of the database. The original prediction approach, based on the representation of binding sites through statistical models was complemented by a new approach that uses known E. coli regulatory sites as the basis for a pattern matching search of regulatory sites. The use of both approaches together resulted in a more intensive exploration of the sequence space of each regulator's binding site. These data should aid researchers in the design of microarray experiments and the interpretation of their results. They should also facilitate studies of Comparative Genomics of the regulatory networks of this group of organisms. | gamma-proteobacterial genome, transcription factor binding site, transcription factor, regulatory network, microarray, comparative genomicis, genome |
is listed by: OMICtools has parent organization: National Laboratory for Scientific Computing; Rio de Janeiro; Brazil has parent organization: National Laboratory for Scientific Computing; Rio de Janeiro; Brazil |
PMID:17088283 | OMICS_01863, nif-0000-03574 | http://www.bioinfo.cu/Tractor_DB, http://www.tractor.lncc.br, http://www.ccg.unam.mx/tractorDB | SCR_005610 | Tractor_DB | 2026-08-04 09:41:23 | 3 | ||||||
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Alternative Splicing Annotation Project II Database Resource Report Resource Website 1+ mentions |
Alternative Splicing Annotation Project II Database (RRID:SCR_000322) | ASAP II | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. An expanded version of the Alternative Splicing Annotation Project (ASAP) database with a new interface and integration of comparative features using UCSC BLASTZ multiple alignments. It supports 9 vertebrate species, 4 insects, and nematodes, and provides with extensive alternative splicing analysis and their splicing variants. As for human alternative splicing data, newly added EST libraries were classified and included into previous tissue and cancer classification, and lists of tissue and cancer (normal) specific alternatively spliced genes are re-calculated and updated. They have created a novel orthologous exon and intron databases and their splice variants based on multiple alignment among several species. These orthologous exon and intron database can give more comprehensive homologous gene information than protein similarity based method. Furthermore, splice junction and exon identity among species can be valuable resources to elucidate species-specific genes. ASAP II database can be easily integrated with pygr (unpublished, the Python Graph Database Framework for Bioinformatics) and its powerful features such as graph query, multi-genome alignment query and etc. ASAP II can be searched by several different criteria such as gene symbol, gene name and ID (UniGene, GenBank etc.). The web interface provides 7 different kinds of views: (I) user query, UniGene annotation, orthologous genes and genome browsers; (II) genome alignment; (III) exons and orthologous exons; (IV) introns and orthologous introns; (V) alternative splicing; (IV) isoform and protein sequences; (VII) tissue and cancer vs. normal specificity. ASAP II shows genome alignments of isoforms, exons, and introns in UCSC-like genome browser. All alternative splicing relationships with supporting evidence information, types of alternative splicing patterns, and inclusion rate for skipped exons are listed in separate tables. Users can also search human data for tissue- and cancer-specific splice forms at the bottom of the gene summary page. The p-values for tissue-specificity as log-odds (LOD) scores, and highlight the results for LOD >= 3 and at least 3 EST sequences are all also reported. | exon, gene structure, genome, alternative splicing, cancer genome alignment, intron, isoform, orthologous exon, orthologous gene, orthologous intron, protein sequence, splice site, tissue, genome alignment, cancer |
is related to: ASAP: the Alternative Splicing Annotation Project has parent organization: University of California at Los Angeles; California; USA |
NCRR U54 RR021813; NIDCR DE-FC02-02ER63421 |
PMID:17108355 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02572 | SCR_000322 | ASAP II Database, Alternative Splicing Annotation Project II | 2026-08-04 09:40:06 | 2 | |||||
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Microbial Genetics Resource at JGI Resource Report Resource Website |
Microbial Genetics Resource at JGI (RRID:SCR_000570) | JGI Microbial Genetics Program | database, data or information resource | Mission: Dynamically evolve sequencing, finishing, annotation and analysis processes, exploit new technologies, and develop expertise to deliver high quality and high throughput sequence-based microbial science by listening to and responding to DOE Users and scientific community needs. GOALS 1. Expand product catalog and increase sample throughput while maintaining highest quality The MGP has been expanding its product catalog beyond a finished microbial genome and has projected to significantly up ramp throughput for the majority of its current products namely Draft Genomes, Single Cell Genomes, Quick Draft Genomes, Resequencing projects and RNAseq Project. This projected increase in microbial genomes is going hand-in-hand with and has been stimulated by new high throughput technologies and capabilities (de novo microbial Illumina assemblies, single cell genomics, Genologic sample tracking). The increased throughput will support the user community as well as JGI scientists by enabling DOE-relevant science at a grander scale. As the Program aims to generate hundreds of microbial genomes per year, our goal is to scale our production efficiency and maintain our trademark quality to best support our science mission. 2. Expand sequence space One of the ongoing missions of the MGP is to expand the coverage of the phylogenomic sequence space by generating reference genome datasets from highly diverse braches in bacterial and archaeal tree of life. The value of such effort includes the generation of phylogenetic anchors for metagenomic datasets, the improvement of annotation, an increased insight into phylogenetic distribution of functions, the discovery of novel genes, protein families, pathways and a better understanding on evolutionary diversication. 3. Make Single Cell Genomes a robust User product As the vast majority of microbes are uncultured to date, single cell genomics will be a crucial component of the MGP over the next several years to drive not only JGI science but also User community proposed single cell research. Going hand-in-hand are R&D efforts in selective single cell isolations, testing the effects of fixation of single cell sequencing, as well as single cell transcriptomics. 4. Sequence Pangenomes Combining similar genomes together creating pangenomes will allow more compact genome sequence storage and visualization and expedite analysis and annotation. Moreover, the pangenome as a representation of the whole group of organisms may be more representative of a given species within the environment. The MGP thus thrives to enable the sequencing and analysis of pangenomes. Current technology allows the sequencing of one organism strain at a time. Assuming that for most cases, several dozen strains may need to be sequenced in order to generate a more accurate pangenome for every microbial species, it becomes evident that the cost for doing so may be prohibitively high. Our goal here will be to explore new approaches and technologies for generating these pangenomes at a very low cost and analogous to what is the cost today for a single strain. 5. Expand and improve microbial annotation using transcriptomic data To improve annotation of gene structure, establish accurate transcription level and timing, provide information on gene regulation and generate information for expanding understanding of systems biology, the MGP thieves to generate transcriptomics data for larger sets of Bacteria and/or Archaea. This will enable the identification of novel regulator RNAs, as well as facilitate the understanding of uncharacterized protein families. 6. Maintain and evolve a top quality data management system To enable state of the art and world class comparative analysis of internal and external scientific projects, the JGI data integration and visualization management system for comparative analysis of microbial genomes, namely IMG, needs to be maintained and continuously evolved. The system needs to be able to support and integrate all data generated by JGI (WGS, reseq, RNAseq, -other omics data), as well as by the user community, enabling annotation and manual curation of the annotation, comparative analysis, gene-centric and pathway centric analyzes. The system should also facilitate the interation of associated metadata, enable data sharing and distribution, as well as automated data GenBank submissions. Lastly, the system needs to have the ability to scale enabling the annotation of thousands of genomes per year. 7. Drive Flagship projects To stay at the forefront of microbial genomic research, be recognized as such and enable the development new methods and tools, the MGP aims to drive DOE mission relevant flagship projects. Novel tools and methods developed will ultimately serve the user community if proven useful and implemented as part of a larger pipeline. MGP flagship projects are the GEBA and GEBA uncultured projects, as well as the GEBA-RNB, the proposed Microbial Earth and the Microbial Dark Matter Projects. | genomics, microbe, bacteria, archaea, sequencing, annotation, genome, microbial | has parent organization: DOE Joint Genome Institute | DOE | nlx_144369 | SCR_000570 | Microbial Genetics Program - Exploration of Microbial Diversity, Microbial Genetics Program at JGI | 2026-08-04 09:40:10 | 0 | |||||||
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tbvar Resource Report Resource Website |
tbvar (RRID:SCR_001178) | tbvar | database, data or information resource | Database of the variome of Mycobacterium tuberculosis (Mtb) comprising of over 29,000 single nucleotide variations created from re-analyzed data sets corresponding to over 400 isolates of Mtb. Using a systematic computational pipeline, potential functional variants and drug-resistance associated variants have been annotated. The database has an option to annotate variants from clinical re-sequencing of Mtb. | single nucleotide variation, genome, gene annotation, variome, genome variation, gene, variant location |
is listed by: OMICtools has parent organization: CSIR-Institute of Genomics and Integrative Biology; Delhi; India |
Tuberculosis | PMID:24408216 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02180 | SCR_001178 | 2026-08-04 09:40:20 | 0 | ||||||
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SSCprofiler Resource Report Resource Website 1+ mentions |
SSCprofiler (RRID:SCR_001282) | SSCprofiler | data analysis service, analysis service resource, production service resource, service resource | Tool which can be used to identify novel miRNA gene candidates in the human genome. | microrna, gene, genome, sequence, structure, conservation |
is listed by: OMICtools has parent organization: Institute of Molecular Biology and Biotechnology; Heraklion; Greece |
PMID:19324892 | Free, Freely available | OMICS_02055 | SCR_001282 | Sequence Structure and Conservation profiler | 2026-08-04 09:40:21 | 3 | ||||||
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HiPipe Resource Report Resource Website 1+ mentions |
HiPipe (RRID:SCR_001215) | HiPipe | data analysis service, analysis service resource, production service resource, service resource | Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task. | next-generation sequencing, dna, rna, differential expression, mirna, gene fusion, variant, genome, exome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Academia Sinica; Taipei; Taiwan |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02128, biotools:hipipe | https://bio.tools/hipipe | SCR_001215 | HiPipe - High Performance Pipelines for NGS Data Analysis | 2026-08-04 09:40:20 | 2 | ||||||
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Ensembl Metazoa Resource Report Resource Website 10+ mentions |
Ensembl Metazoa (RRID:SCR_000800) | database, data or information resource | Ensembl Genomes project produces genome databases for important species from across taxonomic range, using Ensembl software system. Five sites are now available, one of which is Ensembl Metazoa, which houses metazoan species. | database, genome, metazoan, software, specie, taxonomic, FASEB list |
has parent organization: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: European Bioinformatics Institute |
EMBL - EBI | PMID:21785142 | r3d100011198, nif-0000-33714 | SCR_000800 | EnsemblMetazoa | 2026-08-04 09:40:14 | 37 | |||||||
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Drosophila RNAi Screening Center Resource Report Resource Website 1+ mentions |
Drosophila RNAi Screening Center (RRID:SCR_000733) | DRSC | database, data or information resource | Database that provides free online tools to users to allow the retrieval of information related to the Drosophila genome and allows access to genome-wide and related cell-based screening of Drosophila at Harvard Medical School (for a fee) . Tools available include SnapDragon, and RNAi designer, a heat map tool for viewing screen data, and gene and amplicon search and download tools. The DRSC mainly exists to provide Drosophila genome screening services, including help with assay development and optimization, data and image analysis, and planning of follow-up assays. | genome, screening, drosophila, fly, insect, rnai | has parent organization: Harvard University; Cambridge; United States | NIH Office of the Director R24 OD011176 | PMID:16381918 | nif-0000-02846 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, http://flyRNAi.org/cgi-bin/RNAi_screens.pl | SCR_000733 | Development of Validated Drosophila in vivo RNAi Models of Human Diseases | 2026-08-04 09:40:12 | 2 | |||||
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Archaeal and Bacterial ABC Transporter Database Resource Report Resource Website 1+ mentions |
Archaeal and Bacterial ABC Transporter Database (RRID:SCR_001692) | ABCdb, | database, data or information resource | ABCdb is a public resource devoted to the ATP-binding Cassette (ABC) transporters encoded by completely sequenced prokaryotic genomes. In order to establish, in a complete genome, the repertory of ABC systems, we have to: i) identify the different partners, ii) assemble the partners in putative systems, and iii) classify the system into the correct functional subfamily (Quentin et al., 2002). The main pitfalls were the identification of loosely conserved domains and the assembly of partners encoded by genes dispersed over the chromosome. In order to face the avalanche of newly sequenced genomes, we decided to also feed into the database the raw prediction issued by this automatic procedure, before time consuming review by an expert occurs. Therefore, the database comprises two sections: CleanDb, for data checked by an expert and AutoDb for raw data. The ABC proteins are involved in a wide variety of physiological processes in Archaea, Bacteria and Eucaryota where they are encoded by large families of paralogous genes. The majority of ABC domains energize the transport of compounds across membranes. In bacteria, ABC transporters are involved in the uptake of a wide variety of molecules, as well as in mechanisms of virulence and antibiotic resistance. In eukaryotes, most of them are involved in drug resistance and in human cell, many are associated with diseases. Sequence analysis reveals that members of the ABC superfamily can be organized into sub-families, and suggests that they have diverged from common ancestral forms. A typical ABC transporter system is composed of an assembly of protein domains that serve different functions: i) two Nucleotide Binding Domains (NBD) that energize transport via ATP hydrolysis, ii) two Membrane Spanning Domains (MSD) that act as a membrane channel for the substrate, and iii) for the importer, a Solute Binding Protein (SBP) that confers substrates specificity on the transporter. The different partners of an ABC system are generally encoded by neighboring genes. The database includes information on: * ABC transporters * Protein partners * Protein domains (NBD, MSD and SBP) * Classification of ABC transporters and their protein partners * Taxonomy of the species Each model Protein includes a link to the Peptide sequence, general information extracted from EMBL files, and specific tags to store results of predictions. The results of the annotation procedure are reachable through the class Prediction. The origin of the proteins is modeled as a path through the classes Chromosome, Strain, Species, and Taxon. Assembly and protein compilation tables are also provided for each of the chromosomes ( Assembly and Protein ). | abc transporters, archaea, bacteria, prokaryotic genomes, genome, complete genome | has parent organization: Paul Sabatier University - Toulouse III; Toulouse; France | Centre National de la Recherche Scientifique ; ACI-IMPbio |
PMID:16499625 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02530 | SCR_001692 | Archaeal and Bacterial ABC Systems database | 2026-08-04 09:40:27 | 5 |
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