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on page 1 showing 20 out of 45 results from 1 sources

Cite this (5S Ribosomal RNA Database, RRID:SCR_007545)

URL: http://biobases.ibch.poznan.pl/5SData/

Resource Type: Resource, data or information resource, database

A database on nucleotide sequences of 5S rRNAs and their genes. The database contains 1985 primary structures of 5S rRNA and 5S rDNA, and was last updated in 2002, according to the website. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. The multiple sequence alignments of 5S ribosomal RNAs can be downloaded in TAB-delimited and FASTA formats.

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Cite this (AnimalTFDB, RRID:SCR_001624)

URL: http://www.bioguo.org/AnimalTFDB/

Resource Type: Resource, data or information resource, database

A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading.

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Cite this (Autophagy Database, RRID:SCR_002671)

URL: http://www.tanpaku.org/autophagy/

Resource Type: Resource, data or information resource, database

Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes.

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Cite this (AutoPrime, RRID:SCR_000097)

URL: http://www.autoprime.de/AutoPrimeWeb

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

Server to rapidly design primers for real-time PCR measurement of eukaryotic expression.

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Cite this (Biological Biochemical Image Database, RRID:SCR_003474)

URL: http://bbid.irp.nia.nih.gov/

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

Database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics. The rationale for this collection is that: # Except in a few cases, information on most biological pathways in higher eukaryotes is non-existent, incomplete, or conflicting. # Similar biological pathways differ by tissue context, developmental stages, stimulatory events, or for other complex reasons. This database allows comparisons of different variations of pathways that can be tested empirically. # The goal of this database is to use images created directly by biomedical scientists who are specialists in a particular biological system. It is specifically designed to NOT use average, idealized or redrawn pathways. It does NOT use pathways defined by computer algorithm or information search approaches. # Information on biological pathways in higher eukaryotes generally resides in the images and text of review papers. Much of this information is not easily accessible by current medical reference search engines. # All images are attributable to the original authors. All pathways or other biological systems described are graphic representations of natural systems. Each pathway is to be considered a work in progress. Each carries some degree of error or incompleteness. The end user has the ultimate responsibility to determine the scientific correctness and validity in their particular biological system. Image/pathway submissions are welcome.

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Cite this (CAZy- Carbohydrate Active Enzyme, RRID:SCR_012909)

URL: http://www.cazy.org

Resource Type: Resource, data or information resource, database

Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site.

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Cite this (Cell Cycle Ontology, RRID:SCR_007085)

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

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

An application ontology integrating knowledge about the eukaryotic cell cycle.

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    CELLO

Cite this (CELLO, RRID:SCR_011968)

URL: http://cello.life.nctu.edu.tw/

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

A subCELlular LOcalization predictor based on a multi-class support vector machine (SVM) classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. They combine votes from these classifiers and use the jury votes to determine the final assignment.

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Cite this (Cell-PLoc, RRID:SCR_011966)

URL: http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc/

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

A package of web-servers for predicting subcellular localization of proteins in different organisms.

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    ChIPBase

Cite this (ChIPBase, RRID:SCR_005404)

URL: http://deepbase.sysu.edu.cn/chipbase/

Resource Type: Resource, data or information resource, database

A database for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs (snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase currently includes millions of transcription factor binding sites (TFBSs) among 6 species. ChIPBase provides several web-based tools and browsers to explore TF-lncRNA, TF-miRNA, TF-mRNA, TF-ncRNA and TF-miRNA-mRNA regulatory networks.

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    COG

Cite this (COG, RRID:SCR_007139)

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

Resource Type: Resource, data or information resource, database

A database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be.

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Cite this (cpnDB: A Chaperonin Database, RRID:SCR_002263)

URL: http://www.cpndb.ca/cpnDB/home.php

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

A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.

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Cite this (DBD: Transcription factor prediction database, RRID:SCR_002300)

URL: http://www.transcriptionfactor.org/index.cgi?Home

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

Database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries. Benchmarks of the transcription factor predictions show they are accurate and have wide coverage on a genomic scale. The DBD consists of predicted transcription factor repertoires for 930 completely sequenced genomes.

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Cite this (Eukaryotic Linear Motif, RRID:SCR_003085)

URL: http://elm.eu.org

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

Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.

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Cite this (Eukaryotic Promoter Database, RRID:SCR_002485)

URL: http://www.epd.isb-sib.ch/

Resource Type: Resource, data or information resource, database

Database for an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.

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Cite this (Euk-mPLoc, RRID:SCR_011971)

URL: http://www.csbio.sjtu.edu.cn/bioinf/euk-multi-2/

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

Data analysis service for predicting subcellular localization of eukaryotic proteins including those with multiple sites. Euk-mPLoc covers 22 eukaryotic subcellular locations.

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    GeneTack

Cite this (GeneTack, RRID:SCR_011953)

URL: http://topaz.gatech.edu/GeneTack/cgi/print_page.cgi?fn=db_home.html&title=Frameshift%20Database

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

Tools for frameshift prediction and a frameshift database.

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Cite this (Genomes Online Database, RRID:SCR_002817)

URL: http://www.genomesonline.org/

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

Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data.

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Cite this (Genomicus, RRID:SCR_011791)

URL: http://www.genomicus.biologie.ens.fr/genomicus-72.01/cgi-bin/search.pl

Resource Type: Resource, data or information resource, database

A genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

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Cite this (HomoloGene, RRID:SCR_002924)

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

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

Databse that provides a system for the automatic detection of homologs, including paralogs and orthologs, among the annotated genes of a wide range of completely sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. HomoloGene reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. Information about the HomoloGene build procedure is provided at www.ncbi.nlm.nih.gov/HomoloGene/HTML/homologene_buildproc.html. The HomoloGene Downloader retrieves transcript, protein or genomic sequences for the genes in a HomoloGene group; in the case of genomic sequence, upstream and downstream regions may be specified.

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