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on page 1 showing 20 out of 76 results

    Aegean

Cite this (Aegean, RRID:SCR_015965)

URL: http://standage.github.io/AEGeAn

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.

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    AmiGO

Cite this (AmiGO, RRID:SCR_002143)

URL: http://amigo.geneontology.org/

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

Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium.

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Cite this (ANNOgesic, RRID:SCR_016326)

URL: https://github.com/Sung-Huan/ANNOgesic

Resource Type: Resource, standalone software, data processing software, software application, data analysis software, software resource, software toolkit

Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.

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Cite this (A.nnotate, RRID:SCR_002839)

URL: http://a.nnotate.com/

Resource Type: Resource, software resource, service resource, commercial organization, storage service resource

An online annotation, collaboration and indexing system for documents and images, supporting PDF and MS Office formats. Instead of emailing different versions of a document back and forth you can all comment on a single read-only copy online. Unlike online word processors, the document is displayed in high quality with fonts and layout just like the printed version. It is easy to use and runs in all common web browsers, with no software or plugins to install. Hosted solutions are available for individuals and workgroups. For enterprise users the full system is available for local installation. Special discounts apply for educational use. The FREE hosted solution offers single-user accounts for uploading up to 30 pages per month. Documents can be shared with any number of annotators.

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    APPRIS

Cite this (APPRIS, RRID:SCR_012019)

URL: http://appris.bioinfo.cnio.es/

Resource Type: Resource, data or information resource, database

A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript.

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Cite this (AQnowledge Bookmarklet, RRID:SCR_002501)

URL: http://aqnowledge.com/aqnowledge-semantic-knowledge-navigation-overview.html

Resource Type: Resource, software resource

Bookmarklet suitable for all main browsers, that, when invoked, highlights concepts of scientific significance in text and offers links to many open information resources about any concept highlighted.

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Cite this (Arabidopsis thaliana Protein Interactome Database, RRID:SCR_001896)

URL: http://www.megabionet.org/atpid/webfile/

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

Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.

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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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    barleyGO

Cite this (barleyGO, RRID:SCR_015709)

URL: https://github.com/eead-csic-compbio/barleyGO

Resource Type: Resource, software resource, source code

Perl software script that can annotate barley sequences with Gene Ontology terms inferred by homology. It uses the IBSC2012 barley GO annotation and supports both nucleotide and peptide sequences.

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    Blixem

Cite this (Blixem, RRID:SCR_015994)

URL: http://www.sanger.ac.uk/science/tools/seqtools

Resource Type: Resource, alignment software, image analysis software, data processing software, software resource, software application

Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites.

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    BOLD

Cite this (BOLD, RRID:SCR_004278)

URL: http://www.barcodinglife.com/

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

DNA barcode data with an online workbench that supports data validation, annotation, and publication for specimen, distributional, and molecular data. The data platform consists of three main modules, a data portal, a database of barcode clusters, and data collection workbench. The Public Data Portal provides access to all public barcode data which consists of data generated using the Workbench module as well as data mined from other sources. The Barcode Index Number (BIN) system assigns a unique identifier to each sequence cluster of COI, providing an interim taxonomic system for species in the animal kingdom. The workbench module integrates secure databases with analytical tools to provide a private collaborative environment for researchers to collect, analyze, and publish barcode data and ancillary DNA sequences. This platform also provides an annotation framework that supports tagging and commenting on records and their components (i.e. taxonomy, images, and sequences), allowing for community-based validation of barcode data. By providing specialized services, it aids in the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. Public data records include record identifiers, taxonomy, specimen details, collection information and sequence data. Data that has been publicly released through BOLD can be retrieved manually through the BOLD public interface or automatically through BOLD web services. BOLD analytical tools are available for any data set that exists in BOLD (including publicly available data). Analytical tools can be accessed through the BOLD Project Console under the headings Sequences Analysis or Specimen Aggregates. Some examples include Taxon ID Tree, Alignment Viewer, Distribution Maps, and Image Library.

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Cite this (BrainSpan: Atlas of the Developing Human Brain, RRID:SCR_008083)

URL: http://brainspan.org/

Resource Type: Resource, atlas, expression atlas, reference atlas, data or information resource

An atlas of the developing human brain designed as a foundational resource for studying transcriptional mechanisms involved in human brain development. The atlas consists of a variety of data modalities and data mining tools. It contains RNA sequencing and exon microarray data profiling up to sixteen cortical and subcortical structures across the full course of human brain development, as well as high-resolution neuroanatomical transcriptional profiles of about 300 distinct structures spanning the entire brain for four midgestional prenatal specimens. Also included are a high-resolution in situ hybridization image data covering selected genes and brain regions in developing and adult human brain, and a reference atlas in full color with high-resolution anatomic reference atlases of prenatal (two stages) and adult human brain along with supporting histology, magnetic resonance imaging (MRI) and diffusion weighted imaging (DWI) data.

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    BRENDA

Cite this (BRENDA, RRID:SCR_002997)

URL: http://www.brenda-enzymes.org/

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

Main database of functional biochemical and molecular enzyme data that provides access to seven interconnected databases. It contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. The majority of the data are manually extracted from the primary literature. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synonyms or via a structure search. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are based on text mining methods and represent a complete survey of PubMed abstracts with information on enzymes in different organisms, tissues or organelles. The supplemental database DRENDA provides more than 910 000 new EC number-disease relations in more than 510 000 references from automatic search and a classification of enzyme-disease-related information. KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts. The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes. The biochemical reaction database BKM-react contains non-redundant enzyme-catalyzed and spontaneous reactions and was developed to facilitate and accelerate the construction of biochemical models. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. BRENDA provides viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. The disease text mining part is strongly enhanced. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology. A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models. The enzymes are classified according to the Enzyme Commission list of enzymes. Some 5000 different enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. Although they intend to give a representative overview on the characteristics and variability of each enzyme the Handbook is not a compendium. The reader will have to go to the primary literature for more detailed information. Naturally it is not possible to cover all the numerous literature references for each enzyme (for some enzymes up to 40000) if the data representation is to be concise as is intended. The data collection is being developed into a metabolic network information system with links to Enzyme expression and regulation information. BRENDA SOAP Webservice is available.

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Cite this (BSA4Yeast, RRID:SCR_017113)

URL: https://bsa4yeast.lcsb.uni.lu

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, web service, service resource, software resource

Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs.

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Cite this (Chromosome 7 Annotation Project, RRID:SCR_007134)

URL: http://www.chr7.org

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

Database containing the DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented; the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. The objective of this project is to generate a comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications. There are over 360 disease-associated genes or loci on chromosome 7. A major challenge ahead will be to represent chromosome alterations, variants, and polymorphisms and their related phenotypes (or lack thereof), in an accessible way. In addition to being a primary data source, this site serves as a weighing station for testing community ideas and information to produce highly curated data to be submitted to other databases such as NCBI, Ensembl, and UCSC. Therefore, any useful data submitted will be curated and shown in this database. All Chromosome 7 genomic clones (cosmids, BACs, YACs) listed in GBrowser and in other data tables are freely distributed.

  • From Current Category

Cite this (Clinotator, RRID:SCR_016054)

URL: https://github.com/rbutleriii/Clinotator

Resource Type: Resource, software resource, software application

Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics.

  • From Current Category

Cite this (Clonotator, RRID:SCR_016730)

URL: http://ec2-52-91-98-53.compute-1.amazonaws.com/run/

Resource Type: Resource, image analysis software, data analysis software, data processing software, data access protocol, web service, software application, sequence analysis software, alignment software, software resource

Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data.

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    DAVID

Cite this (DAVID, RRID:SCR_001881)

URL: http://david.abcc.ncifcrf.gov/

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

An integrated biological knowledgebase and comprehensive set of functional annotation tools for investigators to understand biological meaning behind large lists of genes. For any given gene list, DAVID tools are able to: - Identify enriched biological themes, particularly GO terms - Discover enriched functional-related gene groups - Cluster redundant annotation terms - Visualize genes on BioCarta & KEGG pathway maps - Display related many-genes-to-many-terms on 2-D view. - Search for other functionally related genes not in the list - List interacting proteins - Explore gene names in batch - Link gene-disease associations - Highlight protein functional domains and motifs - Redirect to related literatures - Convert gene identifiers from one type to another.

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    dbNSFP

Cite this (dbNSFP, RRID:SCR_005178)

URL: https://sites.google.com/site/jpopgen/dbNSFP

Resource Type: Resource, data or information resource, database

A database for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Version 2.0 is based on the Gencode release 9 / Ensembl version 64 and includes a total of 87,347,043 nsSNVs and 2,270,742 essential splice site SNVs. It compiles prediction scores from six prediction algorithms (SIFT, Polyphen2, LRT, MutationTaster, MutationAssessor and FATHMM), three conservation scores (PhyloP, GERP++ and SiPhy) and other related information including allele frequencies observed in the 1000 Genomes Project phase 1 data and the NHLBI Exome Sequencing Project, various gene IDs from different databases, functional descriptions of genes, gene expression and gene interaction information, etc. Some dbNSFP contents (may not be up-to-date though) can also be accessed through variant tools, ANNOVAR, KGGSeq, UCSC Genome Browser''s Variant Annotation Integrator, Ensembl Variant Effect Predictor and HGMD.

  • From Current Category

Cite this (Direct Infusion Metabolite Database, RRID:SCR_016188)

URL: https://dimedb.ibers.aber.ac.uk/

Resource Type: Resource, data or information resource, database

Database of metabolite structures and annotations. The sources are from multiple existing metabolic and chemical databases such as HMDB, PubChem, CHEBI, BioCyc, and KEGG.

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