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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Genomic Datasharing Resource Report Resource Website 1+ mentions |
Genomic Datasharing (RRID:SCR_005233) | GDS | narrative resource, feed, data or information resource, standard specification, listserv | NIH established expectations for sharing data obtained through NIH-funded genome-wide association studies (GWAS) with the implementation of the GWAS Policy. Information and resources related to the GWAS Policy can be found on this website. | genome-wide association study, genome, data sharing |
is listed by: OMICtools has parent organization: National Institutes of Health |
NIH | OMICS_00272 | SCR_005233 | GWAS, Genome-Wide Association Studies | 2026-07-28 09:41:16 | 5 | |||||||
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MicrobesOnline Resource Report Resource Website 100+ mentions |
MicrobesOnline (RRID:SCR_005507) | MicrobesOnline | service resource, data or information resource, data analysis service, database, software resource, source code, production service resource, analysis service resource | MicrobesOnline is designed specifically to facilitate comparative studies on prokaryotic genomes. It is an entry point for operon, regulons, cis-regulatory and network predictions based on comparative analysis of genomes. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html. | microbe, genome, bacteria, archaea, fungi, prokaryote, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
DOE DE-AC02-05CH11231 | PMID:19906701 | nlx_144607, biotools:microbesonline | https://bio.tools/microbesonline | SCR_005507 | Microbial Genomics Database, Microbes Online | 2026-07-28 09:41:24 | 156 | |||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | software application, service resource, data analysis software, data analysis service, data access protocol, data processing software, software resource, production service resource, web service, analysis service resource | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Union ; Biotechnology and Biological Sciences Research Council ; EMBL |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 | SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-07-28 09:41:21 | 6936 | |||||
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UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | service resource, project portal, data or information resource, database, portal | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase works with: bedGraphToBigWig |
UC BIOTEuropean UnionH ; Alfred P. Sloan Foundation ; David and Lucille Packard Foundation ; NIH ; HHMI ; CISI ; NHGRI ; DOE ; NSF DBI 9809007; NIGMS GM52848 |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu, https://doi.org/10.17616/R3RK5C | SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-07-28 09:41:20 | 10026 | ||||||
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Hepatitis C Virus Database (HCVdb) Resource Report Resource Website 1+ mentions |
Hepatitis C Virus Database (HCVdb) (RRID:SCR_005718) | HCVdb, | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | The Hepatitis C Virus Database (HCVdb) is a cooperative project of several groups with the mission of providing to the scientific community studying the hepatitis C virus a comprehensive battery of informational and analytical tools. The Viral Bioinformatics Resource Center (VBRC), the Immune Epitope Database and Analysis Resource (IEDB), the Broad Institute Microbial Sequencing Center (MSC), and the Los Alamos HCV Sequence Database (HCV-LANL) are combining forces to acquire and annotate data on Hepatitis C virus, and to develop and utilize new tools to facilitate the study of this group of organisms. | hepatitis c, hepatitis c virus, genome, gene, virus, ortholog comparison, ortholog | has parent organization: VBRC | Hepatitis C virus | NIAID contract HHSN266200400036C | nlx_149175 | SCR_005718 | Hepatitis C Viral Database | 2026-07-28 09:41:19 | 4 | ||||||
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BLASTatlas - Mapping of whole genome homology Resource Report Resource Website 10+ mentions |
BLASTatlas - Mapping of whole genome homology (RRID:SCR_005891) | BLASTatlas | software resource, data access protocol, web service | The BLASTatlas is a tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms using either blastp, blastn, tblastn, or blastx. DNA structural information is also included in the atlas to visualize the DNA chromosomal context of regions. Additional information can be added to these plots. The tool is SOAP compliant and WSDL (web services description language) files are available with programming examples available in Perl. The resolution is per-residue or per nucleotide depending on the regime of the blast search: For each annotation in the reference genome, the best hit in the database genome is found using one of the above algorithms. Each matching or mismatching residue/nucleotide of the best hit (based on BLAST score) is then mapped back to the genome sequence, using the coordinates provided in the annotations. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence enabling automation of repeated tasks. This tool can be relevant in many pangenomic as well as in metagenomic studies, by giving a quick overview of clusters of insertion sites, genomic islands and overall homology between a reference sequence and a data set. | genome, homology, dna, proteome, orf, blastp, blastn, tblastn, blastx, residue, nucleotide | has parent organization: Technical University of Denmark; Lyngby; Denmark | PMID:18414733 | nlx_149461 | SCR_005891 | 2026-07-28 09:41:22 | 13 | ||||||||
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VectorBase Resource Report Resource Website 500+ mentions |
VectorBase (RRID:SCR_005917) | VectorBase | service resource, data or information resource, data repository, database, storage service resource | Bioinformatics Resource Center for invertebrate vectors. Provides web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. | blast, clustalw, hmmer, vector, genomics, genome, sequence, population, insecticide resistance, annotation, microarray, gene expression, anatomy, pathogen, human, transcript, transcriptome, protein, proteome, mitochondria sequence, bioinformatics resource center, pathogen, arthropoda, vector control, ontology, software, source code, mitochondrial sequence, data analysis service, image collection, FASEB list |
is recommended by: National Library of Medicine is listed by: re3data.org is related to: Clustal W2 is related to: AnoBase: An Anopheles database is related to: Hmmer has parent organization: European Bioinformatics Institute has parent organization: University of Notre Dame; Indiana; USA |
NIAID ; Evimalar network of excellence 242095; INFRAVEC 228421; European Union |
PMID:22135296 PMID:19028744 PMID:18262474 PMID:18237287 PMID:17145709 |
Restricted | nif-0000-03624, r3d100010880 | https://doi.org/10.17616/R3CK6B | SCR_005917 | VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens, VectorBase, vector base | 2026-07-28 09:41:29 | 835 | ||||
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DiseaseMeth Resource Report Resource Website 10+ mentions |
DiseaseMeth (RRID:SCR_005942) | service resource, data or information resource, data repository, database, storage service resource | Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases. | disease, methylation, dna methylation, genome, gene, epigenetics, epigenomics, methylome, bio.tools |
is listed by: 3DVC is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Harbin Medical University; Heilongjiang; China |
National Natural Science Foundation of China ; Natural Science Foundation of Heilongjiang Province ; State Key Laboratory of Urban Water Resource and Environment ; Scientific Research Fund of Heilongjiang Provincial Education Department |
PMID:22135302 PMID:27899673 |
Free,Freely available | OMICS_01838, nlx_151289, biotools:diseasemeth, SCR_017488 | http://bioinfo.hrbmu.edu.cn/diseasemeth, https://bio.tools/diseasemeth | http://202.97.205.78/diseasemeth/ | SCR_005942 | , Disease Meth-The Human Disease Methylation Database, DiseaseMeth database, DiseaseMeth version 2.0 | 2026-07-28 09:41:23 | 34 | ||||
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NEMBASE Resource Report Resource Website 10+ mentions |
NEMBASE (RRID:SCR_006070) | NEMBASE | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | NEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets. | nematode, transcriptome, expressed sequence tag, protein, cluster, library, sequence, peptide prediction, functional annotation, gene family, gene, annotation, pathway, genome, partigene, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: nematodes.org |
Wellcome Trust ; Hospital for Sick Children ; BBSRC ; MRC ; NERC |
PMID:21550347 PMID:14681449 |
Public | nlx_151476, biotools:nembase4 | https://bio.tools/nembase4 | SCR_006070 | NEMBASE4, NEMBASE4 - Nematode Transcriptome Analyses | 2026-07-28 09:41:32 | 25 | ||||
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VBRC Resource Report Resource Website 10+ mentions |
VBRC (RRID:SCR_005971) | VBRC | analysis service resource, service resource, data or information resource, data repository, data analysis service, database, production service resource, storage service resource | One of eight Bioinformatics Resource Centers nationwide providing comprehensive web-based genomics resources including a relational database and web application supporting data storage, annotation, analysis, and information exchange to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. These centers serve the scientific community and conduct basic and applied research on microorganisms selected from the NIH/NIAID Category A, B, and C priority pathogens that are regarded as possible bioterrorist threats or as emerging or re-emerging infectious diseases. The VBRC provides a variety of analytical and visualization tools to aid in the understanding of the available data, including tools for genome annotation, comparative analysis, whole genome alignments, and phylogenetic analysis. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. | virus, arenaviridae, bunyaviridae, filoviridae, flaviviridae, paramyxoviridae, poxviridae, togaviridae, blast, ortholog, variation, sequence analysis, genome, gene, epidemiology, bioinformatics resource center, phenotype, pathogenesis, pathogen, annotation, genomics |
has parent organization: University of Alabama at Birmingham; Alabama; USA has parent organization: University of Victoria; British Columbia; Canada is parent organization of: Hepatitis C Virus Database (HCVdb) |
NIAID contract HHSN266200400036C | r3d100012088, nif-0000-03632 | https://doi.org/10.17616/R31M1P | SCR_005971 | Viral Bioinformatics Resource Center | 2026-07-28 09:41:31 | 18 | ||||||
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FungiDB Resource Report Resource Website 100+ mentions |
FungiDB (RRID:SCR_006013) | FungiDB | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | FungiDB is a database for functional and evolutionary comparison of fungal genomes. FungiDB is a functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center (http://EuPathDB.org). FungiDB uses the same infrastructure and user interface as EuPathDB, which allows for sophisticated and integrated searches to be performed using an intuitive graphical system. The current release of FungiDB contains genome sequence and annotation from 18 species spanning several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal "Zygomycete" lineage Mucormycotina. Additionally, FungiDB contains cell cycle microarray data, hyphal growth RNA-sequence data and yeast two hybrid interaction data. The underlying genomic sequence and annotation combined with functional data, additional data from the FungiDB standard analysis pipeline and the ability to leverage orthology provides a powerful resource for in silico experimentation. | genomics, functional genomics, genome, microarray, genome sequence, annotation, rna sequence, orthology, FASEB list | has parent organization: Eukaryotic Pathogen Database Resources | Burroughs Wellcome Fund ; Alfred P. Sloan Foundation |
PMID:22064857 | Much of the data in FungiDB is provided by independent researchers. Please cite them if you use their data. | nlx_151401, r3d100011906 | https://doi.org/10.17616/R35K9M | SCR_006013 | FungiDB - Fungi Genomics Resources | 2026-07-28 09:41:30 | 250 | ||||
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Federation of International Mouse Resources Resource Report Resource Website 1+ mentions |
Federation of International Mouse Resources (RRID:SCR_006137) | FIMRe | data or information resource, community building portal, topical portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7, 2022. Federation of International Mouse Resources (FIMRe) is a collaborating group of Mouse Repository and Resource Centers worldwide whose collective goal is to archive and provide strains of mice as cryopreserved embryos and gametes, ES cell lines, and live breeding stock to the research community. Goals of the Federation of International Mouse Resources: * Coordinate repositories and resource centers to: ** archive valuable genetically defined mice and ES cell lines being created worldwide ** meet research demand for these genetically defined mice and ES cell lines * Establish consistent, highest quality animal health standards in all resource centers * Provide genetic verification and quality control for genetic background and mutations * Provide resource training to enhance user ability to utilize cryopreserved resources | embryo, gamete, embryonic stem cell, embryonic stem cell line, live breeding stock, live mouse, resource center, international network, mouse model, human disease, gene, genome, biomaterial supply resource, cell repository, organism supplier, biospecimen repository, mutation, cryopreserved |
is related to: Jackson Laboratory is related to: Mutant Mouse Resource and Research Center is related to: European Mouse Mutant Archive is related to: RIKEN BioResource Center has parent organization: Mouse Genome Informatics (MGI) |
PMID:16688526 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_151627 | SCR_006137 | Federation of International Mouse Resources (FIMRe) | 2026-07-28 09:41:33 | 4 | ||||||
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GeneVito Resource Report Resource Website |
GeneVito (RRID:SCR_006211) | GeneVito | data visualization software, software resource, software application, data processing software | A JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of poor annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. GeneViTo has already been applied to visualize the genomes of two microbial organisms: the bacterion Chlamydia trachomatis and the archaeon Methanococcus jannaschii. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment (Java 1.4.1) is already installed in the system. | java, genome-wide analysis, genome, visualization, gene, function, structure, dna, protein sequence, genomic, proteomic | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | PMID:14594459 | Free for academic use, Acknowledgement requested | nlx_151776 | SCR_006211 | GeneVito: Genome Visualization Tool, GeneViTo (Genome Visualization Tool), Genome Visualization Tool | 2026-07-28 09:41:29 | 0 | ||||||
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Deciphering Developmental Disorders Resource Report Resource Website 10+ mentions |
Deciphering Developmental Disorders (RRID:SCR_006171) | DDD | service resource, research forum portal, disease-related portal, data or information resource, biospecimen repository, material storage repository, storage service resource, topical portal, portal | The Deciphering Developmental Disorders (DDD) study aims to find out if using new genetic technologies can help doctors understand why patients get developmental disorders. To do this we have brought together doctors in the 23 NHS Regional Genetics Services throughout the UK and scientists at the Wellcome Trust Sanger Institute, a charitably funded research institute which played a world-leading role in sequencing (reading) the human genome. The DDD study involves experts in clinical, molecular and statistical genetics, as well as ethics and social science. It has a Scientific Advisory Board consisting of scientists, doctors, a lawyer and patient representative, and has received National ethical approval in the UK. Over the next few years, we are aiming to collect DNA and clinical information from 12,000 undiagnosed children in the UK with developmental disorders and their parents. The results of the DDD study will provide a unique, online catalogue of genetic changes linked to clinical features that will enable clinicians to diagnose developmental disorders. Furthermore, the study will enable the design of more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with developmental disorders. Over time, the work will also improve understanding of how genetic changes cause developmental disorders and why the severity of the disease varies in individuals. The Sanger Institute will contribute to the DDD study by performing genetic analysis of DNA samples from patients with developmental disorders, and their parents, recruited into the study through the Regional Genetics Services. Using microarray technology and the latest DNA sequencing methods, research teams will probe genetic information to identify mutations (DNA errors or rearrangements) and establish if these mutations play a role in the developmental disorders observed in patients. The DDD initiative grew out of the groundbreaking DECIPHER database, a global partnership of clinical genetics centres set up in 2004, which allows researchers and clinicians to share clinical and genomic data from patients worldwide. The DDD study aims to transform the power of DECIPHER as a diagnostic tool for use by clinicians. As well as improving patient care, the DDD team will empower researchers in the field by making the data generated securely available to other research teams around the world. By assembling a solid resource of high-quality, high-resolution and consistent genomic data, the leaders of the DDD study hope to extend the reach of DECIPHER across a broader spectrum of disorders than is currently possible. | microarray, sequencing, child, genome, chromosome, dna sequencing, ethics, interview, dna, saliva, clinical, genetics, gene, diagnosis, phenotype, clinical data, FASEB list |
is related to: DECIPHER has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Genetic disorder, Parent, Neurodevelopmental disorder, Congenital anomaly, Abnormal growth, Dysmorphic feature, Unusual behavioral phenotype | Wellcome Trust ; Health Innovation Challenge Fund |
PMID:21679367 | nlx_151673 | SCR_006171 | Deciphering Developmental Disorders (DDD) | 2026-07-28 09:41:31 | 42 | |||||
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VizHub Resource Report Resource Website 1+ mentions |
VizHub (RRID:SCR_006209) | VizHub | service resource, data or information resource, data analysis service, production service resource, analysis service resource, portal | A visualization hub displaying sequencing data from the Roadmap Epigenomics project. It hosts high volume of tracks from ENCODE and Roadmap Epigenomics projects, supports multiple organisms, visualizes chromatin-interaction data (e.g. Hi-C), performs gene set view, gene plot, and many others. All delivered on the web at high performance. | epigenomics, neandertal, genome, visualization, browser, sequencing |
uses: UCSC Genome Browser uses: Roadmap Epigenomics Project uses: ENCODE is related to: WashU Epigenome Browser has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Roadmap Epigenomics Project |
nlx_151756 | SCR_006209 | Roadmap Epigenomics Visualization Hub, Visualization Hub | 2026-07-28 09:41:33 | 6 | ||||||||
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Pig Genome Database Resource Report Resource Website |
Pig Genome Database (RRID:SCR_006367) | PGD | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Database facilitating information integration and mining within the pig and across species of all genomics / genetics research results accumulated over the years including pig gene expression, quantitative trait loci (QTL), candidate gene, and whole genome association study (WGAS) results. The key functions developed so far include pig gene pages (a centralized gene search tool), a local copy of Biomart (for customizable genome information queries), genome feature alignment tools (Pig QTLdb and Gbrowse), integrated gene expression information (ANEXDB and ESTdb), a dedicated pig genome and gene set BLAST server, and virtual comparative map database and tools (VCmap). By developing the PGD, it is our aim to collaboratively utilize existing databases and tools via networked functions, such as web services, database API, etc., to maximize the potential of all related databases through the PGD implementation. | gene expression, quantitative trait loci, candidate gene, whole genome association study, genome, chromosome, dna, trait, marker | has parent organization: NAGRP Bioinformatics Coordination Program | United States Department of Agriculture | nlx_152113 | SCR_006367 | 2026-07-28 09:41:35 | 0 | ||||||||
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Proteome Commons Resource Report Resource Website 10+ mentions |
Proteome Commons (RRID:SCR_006234) | Proteome Commons | service resource, community building portal, data or information resource, data repository, database, software resource, storage service resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication. | proteomics, protein, peptide, data sharing, data, tool, news, annotation, proteome, genome |
is listed by: re3data.org has parent organization: University of Michigan; Ann Arbor; USA is parent organization of: Proteome Commons Tranche repository |
NCI ; Clinical Proteomics Technologies for Cancer ; NCRR P41-RR018627 |
PMID:20356086 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151800 | SCR_006234 | ProteomeCommons.org, ProteomeCommons | 2026-07-28 09:41:32 | 12 | |||||
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Phytozome Resource Report Resource Website 1000+ mentions |
Phytozome (RRID:SCR_006507) | Phytozome | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | A comparative platform for green plant genomics. Families of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology / paralogy relationships as well as clade specific genes and gene expansions. As of release v9.1, Phytozome provides access to forty-one sequenced and annotated green plant genomes which have been clustered into gene families at 20 evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genome, genomics, plant, green plant, cluster sequence, alignment, gene, node, cluster, blast, blat, biomart, peptide homolog, gene ancestry, sequence, annotation, gene structure, gene family, genome organization, comparative genomics, physiology, comparative, bio.tools, FASEB list |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: Plant Co-expression Annotation Resource has parent organization: DOE Joint Genome Institute has parent organization: Lawrence Berkeley National Laboratory |
Gordon and Betty Moore Foundation ; DOE DE-AC02-05CH11231 |
PMID:22110026 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:phytozome, nlx_151490, r3d100010850 | https://bio.tools/phytozome, https://doi.org/10.17616/R38021 | SCR_006507 | 2026-07-28 09:41:35 | 3108 | |||||
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NAGRP Bioinformatics Coordination Program Resource Report Resource Website 50+ mentions |
NAGRP Bioinformatics Coordination Program (RRID:SCR_006564) | NAGRP Bioinformatics Coordination Program | data or information resource, service resource, topical portal, portal | We at NRSP-8 bioinformatics coordination program strive to serve the animal genomics research community to better use computer tools and methods, to best utilize available resources, and in working with researchers in the community, to effectively share, combine, manage, manipulate, and analyze information from genomics/genetics studies. This site is designed as an information center to serve the national animal genome research projects of cattle, chicken, pigs, sheep, horse, and aquaculture species. This is home to databases and web sites (being) built for structural, functional and application oriented studies of the animal genomics, to serve the purpose of research, education and related activities in the scientific, industrial and educational communities in the states and world wide. The challenges in bioinformatics support/research for animal genomics may involve * Effective data collection, organization and management * Rapid development of most needed bioinformatics tools and resources * Efficient use of these tools for innovative data analysis Projects: * Animal Trait Ontology (ATO) Project * Virtual Comparative Genomics * The Past, the Current, and the Potentials * Collaborative and Hosted Works | genome, bioinformatics, genomics, sequencing, aquaculture species, computing |
has parent organization: Iowa State University; Iowa; USA is parent organization of: CateGOrizer is parent organization of: Pig Genome Database is parent organization of: Animal QTLdb |
USDA | nlx_149170 | SCR_006564 | USDA NRSP-8 Program Bioinformatics Coordination Project, NAGRP NRSP-8 Bioinformatics Coordination Program, National Animal Genome Research Program NRSP-8 Bioinformatics Coordination Program, National Animal Genome Research Program Bioinformatics Coordination Project | 2026-07-28 09:41:35 | 84 | |||||||
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Genome Reference Consortium Resource Report Resource Website 10+ mentions |
Genome Reference Consortium (RRID:SCR_006553) | GRC | data or information resource, organization portal, database, consortium, portal | Consortium that puts sequences into a chromosome context and provides the best possible reference assembly for human, mouse, and zebrafish via FTP. Tools to facilitate the curation of genome assemblies based on the sequence overlaps of long, high quality sequences. | sequnence, chromosome, reference, assembly, human, mouse, zebrafish, genome, sequence, overlap |
is related to: Zebrafish Genome Project has parent organization: NCBI |
NIH | nif-0000-20983 | http://genomereference.org | http://www.ncbi.nlm.nih.gov/genome/assembly/grc/index.shtml | SCR_006553 | Genome Reference Consortium | 2026-07-28 09:41:35 | 42 |
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