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on page 1 showing 20 out of 38 results

Cite this (1000 Fungal Genome Project, RRID:SCR_016463)

URL: https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf

Resource Type: Resource, topical portal, data access protocol, database, web service, organism-related portal, portal, software resource, project portal, data or information resource

Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.

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    JASPAR

Cite this (JASPAR, RRID:SCR_003030)

URL: http://jaspar.genereg.net

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

Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval.

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Cite this (Fungal Genome Initiative, RRID:SCR_003169)

URL: http://www.broad.mit.edu/annotation/fungi/fgi/

Resource Type: Resource, data set, data or information resource

Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics.

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    LMAT

Cite this (LMAT, RRID:SCR_004646)

URL: https://computation-rnd.llnl.gov/lmat/

Resource Type: Resource, software resource

Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads.

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    AFTOL

Cite this (AFTOL, RRID:SCR_004650)

URL: http://www.aftol.org/

Resource Type: Resource, data repository, biospecimen repository, data set, service resource, storage service resource, data or information resource, material storage repository

To enhance the understanding of the evolution of the Kingdom Fungi, 1500+ species were sampled for eight gene loci across all major fungal clades, plus a subset of taxa for a suite of morphological and ultrastructural characters with resulting data: AFTOL Molecular Database (generated by WASABI - Web Accessible Sequence Analysis for Biological Inference), Blast search the AFTOL Database (generated by WASABI), AFTOL primers (generated by WASABI), AFTOL primers by species (generated by WASABI), AFTOL alignments, and the AFTOL Structural and Biochemical Database. Users may submit samples to the AFTOL project. AFTOL is a collaboration centered around four universities in the United States: Duke University (Francois Lutzoni and Rytas Vilgalys), Clark University (David Hibbett), Oregon State University (Joey Spatafora), and University of Minnesota (David McLaughlin). Participants throughout the world have donated vouchers, taxon samples, and gene sequences. The aim of the project is to reconstruct the fungal tree of life using all available data for eight loci (nuclear ribosomal DNA: LSU, SSU, ITS (including 5.8s, ITS1 and ITS2); RNA polymerase II: RPB1, RPB2; elongation factor 1-alpha; mitochondrial SSU rDNA, and mitochondrial ATP synthase protein subunit 6). A further objective of this study is to summarize and integrate current knowledge regarding fungal subcellular features within this new phylogenetic framework. The name of the bioinformatic package developed for AFTOL is WASABI which provides an efficient communication platform to facilitate the collection and dissemination of molecular data to (and from) the laboratories and participants. All molecular data can be viewed, downloaded, verified, and corrected by the participants of AFTOL. A central goal of the WASABI interface is to establish an automated analysis framework that includes basecalling of newly generated chromatograms, contig assembly, quality verification of sequences (including a local BLAST), sequence alignment, and congruence test. Gene sequences that pass all tests and are finally verified by their authors will undergo automated phylogenetic analysis on a regular schedule. Although all steps are initially carried out noninteractively, the users can verify and correct the results at any step and thus initiate the reanalysis of dependent data.

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    NBC

Cite this (NBC, RRID:SCR_004772)

URL: http://nbc.ece.drexel.edu/

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

Webserver for taxonomic classification of metagenomic reads.

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    GOblet

Cite this (GOblet, RRID:SCR_006998)

URL: http://goblet.molgen.mpg.de/cgi-bin/goblet2008/goblet.cgi

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

Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms.

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Cite this (Fungal Gross Anatomy Ontology, RRID:SCR_010322)

URL: http://purl.bioontology.org/ontology/FAO

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

A structured controlled vocabulary for the anatomy of fungi.

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    BaCelLo

Cite this (BaCelLo, RRID:SCR_011965)

URL: http://gpcr.biocomp.unibo.it/bacello/

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

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

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    OrthoDB

Cite this (OrthoDB, RRID:SCR_011980)

URL: http://cegg.unige.ch/orthodb7

Resource Type: Resource, data or information resource, database

Database of orthologous protein-coding genes across 64 vertebrates, 57 arthropods, 175 fungi, 14 basal metazoans, and 1115 bacteria.

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    WegoLoc

Cite this (WegoLoc, RRID:SCR_001402)

URL: http://www.btool.org/WegoLoc

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

Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information.

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    ATCC

Cite this (ATCC, RRID:SCR_001672)

URL: http://www.atcc.org/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, biomaterial supply resource, standard specification, narrative resource, international standard specification, service resource, storage service resource, reagent supplier, data or information resource, material resource, material storage repository

Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.

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Cite this (Protein Lounge, RRID:SCR_002117)

URL: http://www.proteinlounge.com

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

Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal.

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    GRBio

Cite this (GRBio, RRID:SCR_002228)

URL: http://grbio.org/

Resource Type: Resource, data access protocol, database, web service, people resource, software resource, data or information resource

Database of biological collections in natural history museums, herbaria, and other biorepositories resulting from a merger of Index Herbariorum (IH), Biodiversity Collections Index (BCI) and biorepositories.org. It contains more than 14,000 records for biorepository institutions, their collections, and staff members. Their two main goals are to improve access to information about biorepositories, the collections and specimens they house, and the researchers and collection managers who work there; and to facilitate electronic linkages to this information through web services that will rely on unique identifiers assigned to biorepositories and collections. The Consortium for the Barcode of Life (CBOL) has developed and will manage GRBio in collaboration with IH and BCI and in consultation with GBIF and NCBI. GRBio includes four categories of data records that provide information on: * Institutional repositories such as museums, herbaria, botanical gardens, zoos, biomedical research institutes and culture centers; * Institutional collection records such as the bird, algal or insect collections within an institutional repository; * Personal collections such as field samples held by a researcher before they have been accessioned into an institutional collection, or privately owned specimens held by non-researchers; and * Staff members at institutional repositories GRBio operates as a moderated community-curated resource. The community is invited to check and update their records and to register institutions, collections and staff members that have not already been registered. GRBio offers registration of institutional collections, "personal" research collections that have not yet been accessioned into an institutional repository, and privately owned collections.

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Cite this (WoLF PSORT, RRID:SCR_002472)

URL: http://www.genscript.com/psort/wolf_psort.html

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

Data analysis service for protein subcellular localization prediction.

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Cite this (MapViewer, RRID:SCR_003092)

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

Resource Type: Resource, data or information resource, database

Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.

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Cite this (Proteome Analyst Specialized Subcellular Localization Server, RRID:SCR_003143)

URL: http://webdocs.cs.ualberta.ca/~bioinfo/PA/Sub/

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

Web server specialized to predict the subcellular localization of proteins using established machine learning techniques.

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    PHI-base

Cite this (PHI-base, RRID:SCR_003331)

URL: http://www.phi-base.org/

Resource Type: Resource, data or information resource, database

Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).

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Cite this (Protein Clusters, RRID:SCR_003459)

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

Resource Type: Resource, data or information resource, database

Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP

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Cite this (Cell Type Ontology, RRID:SCR_004251)

URL: http://cellontology.org

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

Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.

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