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on page 1 showing 20 out of 681 results

    3DBar

Cite this (3DBar, RRID:SCR_008896)

URL: http://www.3dbar.org

Resource Type: Resource, production service resource, analysis service resource, reference atlas, software resource, service resource, atlas, data or information resource

Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML

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Cite this (3D-Interologs, RRID:SCR_003101)

URL: http://gemdock.life.nctu.edu.tw/3D-Interologs

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

Database of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins.

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Cite this (ACGT Inc., RRID:SCR_001026)

URL: http://www.acgtinc.com

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

Company which provides a suite of molecular biology and genomic services, including DNA sequencing by Sanger and Next Generation Sequencing. All services are offered at a research, GLP or clinical grade levels.

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    ADaCGH

Cite this (ADaCGH, RRID:SCR_010916)

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

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

A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/

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Cite this (ADDA - Automatic Domain Decomposition Algorithm, RRID:SCR_007546)

URL: http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb

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

This is a web interface for ADDA, an automatic algorithm for domain decomposition and clustering of all protein domain families. We use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model. ADDA is downloadable. There are three ways in which you can retrieve a protein sequence and its domains from ADDA. Sequences can be located using sequence identifiers and/or accession numbers, using a identical fragment lookup, or by running BLAST against all sequences in ADDA. ADDA is a protein sequence clustering algorithm. It takes a set of sequences and returns domain families. ADDA has two steps corresponding to the two aspects of the protein sequence clustering domain. First, ADDA splits protein sequences into domains. The idea behind ADDA is in principle the application of Occam''s razor; the goal is to describe the diversity of protein sequences with a minimal set of protein domains. The algorithm behind ADDA approximates this minimal set. In practice ADDA works by looking at where BLAST alignments are located on the sequence and splits the sequences, so that as few as possible alignments are cut by domain boundaries and that as many alignments as possible stretch over complete domains. Secondly, ADDA takes all the domains and then arranges them in a minimum spanning tree, where the similarity between two domains is determined by their relative overlap given a BLAST alignment. Each link in the tree is then checked by a pairwise profile-profile comparison and links below a threshold are removed. The remaining connected components are then taken to represent protein domain families.

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    ADGO

Cite this (ADGO, RRID:SCR_006343)

URL: http://www.btool.org/ADGO2

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

A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.

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Cite this (Affymetrix Gene Expression Service Lab, RRID:SCR_008396)

URL: http://ipmb.sinica.edu.tw/affy/

Resource Type: Resource, organization portal, material analysis service, analysis service resource, production service resource, laboratory portal, service resource, portal, data or information resource

Affymetrix Gene Expression Service Lab, AGESL was established by IPMB, IMB and IBS, Academia Sinica and opened for service in June 2004. The lab provides a full service from quality control of customer-provided RNA samples to raw data acquisition, including Affymetrix recommended QC procedures, cDNA synthesis, in vitro transcription, fragmentation, hybridization, washing, staining and scanning. Sponsors: This resource is supported by Affymetrix, Inc. Keywords: Gene, Expression, Service, Laboratory, RNA, Data, Synthesis, cDNA, In vitro, Transcription, Fragmentation, Hybrdization, Washing, Staining, Scanning,

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Cite this (Aged Rodent Tissue Arrays, RRID:SCR_007332)

URL: http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook/tissue-arrays

Resource Type: Resource, biomaterial analysis service, analysis service resource, service resource, production service resource, material analysis service

Offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbers

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Cite this (Aggrescan: The Hot Spot Finder, RRID:SCR_008403)

URL: http://bioinf.uab.es/aggrescan/

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

Web-based tool for identifying hot spots of aggregation in polypeptides. Aggrescan uses an aggregation-propensity scale for natural amino acids derived from in vivo experiments and on the assumption that short and specific sequence stretches modulate protein aggregation. The algorithm is shown to identify a series of protein fragments involved in the aggregation of disease-related proteins and to predict the effect of genetic mutations on their deposition propensities. It also provides new insights into the differential aggregation properties displayed by globular proteins, natively unfolded polypeptides, amyloidogenic proteins and proteins found in bacterial inclusion bodies.

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Cite this (Agile Protein Interactomes DataServer, RRID:SCR_008871)

URL: http://apid.dep.usal.es

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

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.

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    agriGO

Cite this (agriGO, RRID:SCR_006989)

URL: http://bioinfo.cau.edu.cn/agriGO/

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

A web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online tool

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Cite this (Algal Functional Annotation Tool, RRID:SCR_012034)

URL: http://pathways.mcdb.ucla.edu/algal/

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

Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest.

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Cite this (Align-GVGD, RRID:SCR_010772)

URL: http://agvgd.iarc.fr/index.php

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

A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral.

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Cite this (AllerHunter: Cross-reactive Allergen Prediction Home, RRID:SCR_002950)

URL: http://tiger.dbs.nus.edu.sg/AllerHunter

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

A cross-reactive allergen prediction program built on a combination of Support Vector Machine (SVM) and pairwise sequence similarity. Cross-reactivity is based on similarity of proteins to allergens. However, not all proteins with similar sequence or structure to known allergens are cross-reactive allergens. AllerHunter aims to predict allergens and non-allergens with high sensitivity and specificity, without compromising efficiency at classification of proteins with similar sequence to known allergens. There are distinct differences between prediction of allergenicity and cross-reactivity of allergens. Allergenicity is the immunogenic potential of an allergen to induce IgE antibody production, whereas cross-reactivity is the potential of a substance to bind to IgE previously induced by a known allergen. It is difficult to predict allergenicity because causes of immunogenicity of allergens are still not completely clear. However it is possible to predict cross-reactivity since it implies similarity in IgE binding sites. Please provide protein sequence in fasta format.

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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 (AmphoraNet, RRID:SCR_005009)

URL: http://amphoranet.pitgroup.org/

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

Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample.

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Cite this (AMYL-PRED, RRID:SCR_006185)

URL: http://bioinformatics.biol.uoa.gr/AMYLPRED/

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

A web tool using the consensus prediction method for identifying possible amyloidogenic regions in protein sequences. This tool uses an assortment of different methods that have been found or specifically developed to predict features related to the formation of amyloid fibrils. The consensus of these methods is defined as the the hit overlap of at least two out of five methods and it is the primary output of the program. However, the individual predictions of these methods are also made available in the form of a text file, maintained on the server for 1 (one) day. Consequently, the tool predicts probable amyloidogenic determinants for a given amino acid sequence of a peptide or protein.

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    Ancora

Cite this (Ancora, RRID:SCR_001623)

URL: http://ancora.genereg.net/

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

Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements.

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Cite this (ApiDB PlasmoDB, RRID:SCR_013331)

URL: http://PlasmoDB.org

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

PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria. It brings together data provided by numerous laboratories worldwide (see the Data Sources page), and adds its own data analysis. PlasmoDB is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB Bioinformatics Resource Center (BRC) umbrella. PlasmoDB contains numerous data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis. Organisms * Annotated genomes: Plasmodium falciparum, Plasmodium vivax, Plasmodium yoelii, Plasmodium berghei, Plasmodium chabaudi, Plasmodium knowlesi * Unannotated genomes: Plasmodium reichenowi, Plasmodium gallinaceum * Others: environmental isolate sequences from numerous species PlasmoDB provides programmatic access to its searches, via REST Web Services.

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Cite this (Arabidopsis thaliana Genome Database, RRID:SCR_001901)

URL: http://www.plantgdb.org/AtGDB/

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

Database providing a sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on gene structure annotation. The current genome assembly displayed at AtGDB is version TAIR9. Annotated gene models are TAIR10. They have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing.

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