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on page 1 showing 20 out of 34 results

    ASAP

Cite this (ASAP, RRID:SCR_001849)

URL: https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points.

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    ASPGD

Cite this (ASPGD, RRID:SCR_002047)

URL: http://www.aspgd.org/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.

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Cite this (Berkeley Bioinformatics Open-Source Projects, RRID:SCR_006704)

URL: http://www.berkeleybop.org/

Resource Type: Resource, software resource, topical portal, portal, data or information resource

The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including the Gene Ontology, OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project. Our group is focused on the development, use, and integration of ontolgies into biological data analysis. Software written or maintained by BBOP is accessible through the site.

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Cite this (Candida Genome Database, RRID:SCR_002036)

URL: http://www.candidagenome.org/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database of genetic and molecular biological information about Candida albicans, a yeast that is an opportunistic pathogen of humans, and about other Candida-related species, such as Candida glabrata. It contains information about genes and proteins; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to a DNA sequence also have Locus Pages. The Locus Page is the central clearinghouse for all information specific to that gene and tools for its analysis, including: * gene name, synonyms, and systematic name * Gene Ontology (GO) annotations * descriptions of the gene and gene product * phenotype of mutations in the gene * chromosomal and contig coordinates * interactive graphical chromosome map and browsing tool * tools for retrieval and analysis of the gene and protein sequences * a curated collection of literature CGD also provides a Gene Ontology, GO, to all its users. GO is a collaborative project involving CGD and other model organism databases to provide controlled vocabularies that are used to describe the molecular function and cellular location of gene products and the biological process in which they are involved. The three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. The development of the ontologies is ongoing in order to incorporate new information. Data submissions are welcome.

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Cite this (DictyBase, RRID:SCR_006643)

URL: http://dictybase.org/

Resource Type: Resource, data analysis service, organism supplier, database, analysis service resource, biomaterial supply resource, biospecimen repository, production service resource, service resource, storage service resource, material storage repository, material resource, data or information resource

Model organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ''''reference genome'''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries.

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    EcoCyc

Cite this (EcoCyc, RRID:SCR_002433)

URL: http://ecocyc.org/

Resource Type: Resource, data or information resource, database

Database for the bacterium Escherichia coli K-12 MG1655, the EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms.

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    ECO

Cite this (ECO, RRID:SCR_002477)

URL: http://www.evidenceontology.org

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2

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    FlyBase

Cite this (FlyBase, RRID:SCR_006549)

URL: http://flybase.org/

Resource Type: Resource, topical portal, organism-related portal, analysis service resource, database, data analysis service, service resource, portal, production service resource, storage service resource, data repository, data or information resource

Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.

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Cite this (GeneDB Lmajor, RRID:SCR_004613)

URL: http://www.genedb.org/Homepage/Lmajor

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Database of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.

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Cite this (GeneDB Pfalciparum, RRID:SCR_006567)

URL: http://www.genedb.org/Homepage/Pfalciparum

Resource Type: Resource, data or information resource, database

Database of the most recent sequence updates and annotations for the P. falciparum genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Plasmodium research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. The P. falciparum 3D7 nuclear genome is 23.3 Mb in size, with a karyotype of 14 chromosomes. The G+C content is approximately 19%. The P. falciparum genome is undergoing re-annotation. This process started in October 2007 with a weeklong workshop co-organized by staff from the Wellcome Trust Sanger Intistute and the EuPathDB team. Ongoing curation and sequence checking is being carried out by the Pathogen Genomics group. Plasmodium falciparum is the most deadly of the five Plasmodium species that cause human malaria. Malaria has a massive impact on human health; it is the worlds second biggest killer after tuberculosis. Around 300 million clinical cases occur each year resulting in between 1.5 - 2.7 million deaths annually, the majority in sub-saharan Africa. It is estimated that 3,000 children under the age of five years fall victim to malaria each day. Around 40% of the worlds population are at risk. In collaboration with EuPathDB, genomic sequence data and annotations are regularly deposited on PlasmoDB where they can be integrated with other datasets and queried using customized queries.

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Cite this (GeneDB Tbrucei, RRID:SCR_004786)

URL: http://www.genedb.org/Homepage/Tbruceibrucei927

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Database of the most recent sequence updates and annotations for the T. brucei genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. T. brucei possesses a two-unit genome, a nuclear genome and a mitochondrial (kinetoplast) genome with a total estimated size of 35Mb/haploid genome. The nuclear genome is split into three classes of chromosomes according to their size on pulsed-field gel electrophoresis, 11 pairs of megabase chromosomes (0.9-5.7 Mb), intermediate (300-900 kb) and minichromosomes (50-100 kb). The T. brucei genome contains a ~0.5Mb segmental duplication affecting chromosomes 4 and 8, which is responsible for some 75 gene duplicates unique to this species. A comparative chromosome map of the duplicons can be accessed here (PubmedID 18036214). Protozoan parasites within the species Trypanosoma brucei are the etiological agent of human sleeping sickness and Nagana in animals. Infections are limited to patches of sub-Saharan Africa where insects vectors of the Glossina genus are endemic. The most recent estimates indicate between 50,000 - 70,000 human cases currently exist, with 17 000 new cases each year (WHO Factsheet, 2006). In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.

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Cite this (go-db-perl, RRID:SCR_005721)

URL: http://search.cpan.org/~cmungall/go-db-perl/

Resource Type: Resource, software resource

Software resource that extends the functionality of go-perl (on which it depends) with GO Database access functionality. go-db-perl comes bundled with various scripts and a shell command line interface that can be used as standalone tools. Installation is more involved than for go-perl; you will need a MySQL database plus the requisite DBI and DBD Perl modules. Full installation instructions are included in the download. go-db-perl is in use both to drive AmiGO and internally within Ensembl. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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Cite this (GO-Module, RRID:SCR_005813)

URL: http://lussierlab.org/GO-Module/GOModule.cgi

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

GO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online tool

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    Gramene

Cite this (Gramene, RRID:SCR_002829)

URL: http://www.gramene.org

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

A curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

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    JCVI CMR

Cite this (JCVI CMR, RRID:SCR_005398)

URL: http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Database of all of the publicly available, complete prokaryotic genomes. In addition to having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes. CMR offers a wide variety of tools and resources, all of which are available off of our menu bar at the top of each page. Below is an explanation and link for each of these menu options. * Genome Tools: Find organism lists as well as summary information and analyses for selected genomes. * Searches: Search CMR for genes, genomes, sequence regions, and evidence. * Comparative Tools: Compare multiple genomes based on a variety of criteria, including sequence homology and gene attributes. SNP data is also found under this menu. * Lists: Select and download gene, evidence, and genomic element lists. * Downloads: Download gene sequences or attributes for CMR organisms, or go to our FTP site. * Carts: Select genome preferences from our Genome Cart or download your Gene Cart genes. The Omniome is the relational database underlying the CMR and it holds all of the annotation for each of the CMR genomes, including DNA sequences, proteins, RNA genes and many other types of features. Associated with each of these DNA features in the Omniome are the feature coordinates, nucleotide and protein sequences (where appropriate), and the DNA molecule and organism with which the feature is associated. Also available are evidence types associated with annotation such as HMMs, BLAST, InterPro, COG, and Prosite, as well as individual gene attributes. In addition, the database stores identifiers from other centers such as GenBank and SwissProt, as well as manually curated information on each genome or each DNA molecule including website links. Also stored in the Omniome are precomputed homology data, called All vs All searches, used throughout the CMR for comparative analysis.

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    MeGO

Cite this (MeGO, RRID:SCR_000110)

URL: http://aclame.ulb.ac.be/Classification/mego.html

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

A Gene Ontology dedicated to the functions of mobile genetic elements. The terms defined are used to annotate phage and plasmid protein families in ACLAME. Note: The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up.

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Cite this (Mouse Genome Informatics, RRID:SCR_006460)

URL: http://www.informatics.jax.org

Resource Type: Resource, data or information resource, database

An international database for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Its primary mission is to facilitate the use of the mouse as a model system for understanding human biology and disease. MGI creates and maintains an integrated representation of mouse genetic, genomic, expression, and phenotype data and develops definitive reference data set and consensus data views. MGI also synthesizes comparative genomic data between the mouse and other mammals, maintains a set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides extensive technical support for database users. The projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.

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Cite this (NCBI Protein, RRID:SCR_003257)

URL: http://www.ncbi.nlm.nih.gov/protein

Resource Type: Resource, data or information resource, database

Database of protein sequences related to biological structure and function from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, Protein Information Resource (PIR), Protein Research Foundation (PRF), and Protein Data Bank (PDB).

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    NCBI

Cite this (NCBI, RRID:SCR_006472)

URL: http://www.ncbi.nlm.nih.gov

Resource Type: Resource, portal, data or information resource

A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.

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    PomBase

Cite this (PomBase, RRID:SCR_006586)

URL: http://www.pombase.org/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation, mailing lists, and welcomes data submissions.

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