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on page 1 showing 20 out of 33 results

Cite this (3D Ribosomal Modification Maps Database, RRID:SCR_003097)

URL: http://people.biochem.umass.edu/fournierlab/3dmodmap/

Resource Type: Resource, data or information resource, database

Database of maps showing the sites of modified rRNA nucleotides. Access to the rRNA sequences, secondary structures both with modification sites indicated, 3D modification maps and the supporting tables of equivalent nucleotides for rRNA from model organisms including yeast, arabidopsis, e. coli and human is provided. This database complements the Yeast snoRNA Database at UMass-Amherst and relies on linking to some content from that database, as well as to others by colleagues in related fields. Therefore, please be very cognizant as to the source when citing information obtained herein. Locations of modified rRNA nucleotides within the 3D structure of the ribosome.

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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 (Bacteriome.org, RRID:SCR_001934)

URL: http://www.bacteriome.org

Resource Type: Resource, data or information resource, database

Database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Presently the resource offers access to two types of network: * A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework * Two networks of experimentally derived protein-protein interactions - a "core" network consisting of interactions deemed to be of "high quality"; and an "extended" network which extends the "core" network by including interactions for which experimental evidence is less strong.

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Cite this (BiblioSpec, RRID:SCR_004349)

URL: http://proteome.gs.washington.edu/software/bibliospec/documentation/index.html

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

BiblioSpec enables the identification of peptides from tandem mass spectra by searching against a database of previously identified spectra. This suite of software tools is for creating and searching MS/MS peptide spectrum libraries. BiblioSpec is available free of charge for noncommercial use through an interactive web-site at http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/bibliospec.php The BiblioSpec package contains the following programs: * BlibBuild creates a library of peptide MS/MS spectra from MS2 files. * BlibFilter removes redundant spectra from a library. * BlibSearch searches a spectrum library for matches to query spectra, reporting the results in an SQT file. In addition to the primary programs, the following auxiliary programs are available: * BlibStats writes summary statistics describing a library. * BlibToMS2 writes a library in MS2 file format. * BlibUpdate adds, deletes, or annotates spectra. * BlibPpMS2 processes spectra (bins peaks, removes noise, normalizes intensity) as done in BlibSearch and prints the resulting spectra to a text file. Several reference libraries are available for download. These libraries are updated regularly and are for use under the Linux operating system. You will find libraries for * Escherichia coli * Saccharomyces cerevisiae * Caenorhabditis elegans

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Cite this (BiGG Database, RRID:SCR_005809)

URL: http://bigg.ucsd.edu/

Resource Type: Resource, data or information resource, database

A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

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    BioCyc

Cite this (BioCyc, RRID:SCR_002298)

URL: http://biocyc.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

A collection of Pathway/Genome Databases which describes the genome and metabolic pathways of a single organism. The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. They also include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received. Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating. Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating. Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 967 DBs in Tier 3. The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site.

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    Colibri

Cite this (Colibri, RRID:SCR_007606)

URL: http://genolist.pasteur.fr/Colibri/

Resource Type: Resource, data or information resource, database

Database dedicated to the analysis of the genome of Escherichia coli. Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). The data contained in Colibri originates from two major sources of information, the reference genomic DNA sequence from the E. coli Genome Project and the feature annotations from the EcoGene data collection.

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Cite this (CoryneRegNet, RRID:SCR_002255)

URL: http://www.coryneregnet.de

Resource Type: Resource, data or information resource, database

Reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks. It generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure.

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Cite this (DNAtraffic, RRID:SCR_008886)

URL: http://dnatraffic.ibb.waw.pl/

Resource Type: Resource, data or information resource, database

DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on diseases related to the assembled human proteins. Database is richly annotated in the systemic information on the nomenclature, chemistry and structure of the DNA damage and drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA metabolism pathway analysis. Database includes illustrations of pathway, damage, protein and drug. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines it has to be extensively linked to numerous external data sources. Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. DNAtraffic database is freely available and can be queried by the name of DNA network process, DNA damage, protein, disease, and drug.

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Cite this (DRC - Database of Ribosomal Crosslinks, RRID:SCR_007628)

URL: http://owww.molgen.mpg.de/~ag_ribo/ag_brimacombe/drc/

Resource Type: Resource, data or information resource, database

A database of published cross-link data of the E. coli ribosome. The website provides information on rRNA-rRNA cross-links, rRNA-rProteins cross-links, cross-links between ribosomal proteins, tRNA-ribosome cross-links, growing peptide-ribosome cross-links, factors-ribosome cross-links, and mRNA-ribosome cross-links. All data are presented in tables.

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    EchoBASE

Cite this (EchoBASE, RRID:SCR_002430)

URL: http://www.ecoli-york.org/

Resource Type: Resource, data or information resource, database

A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium.

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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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    EcoGene

Cite this (EcoGene, RRID:SCR_002437)

URL: http://ecogene.org/

Resource Type: Resource, data or information resource, database

Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries.

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Cite this (EcoliWiki, RRID:SCR_010656)

URL: http://ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki

Resource Type: Resource, wiki, data access protocol, web service, narrative resource, software resource, data or information resource

A component of EcoliHub, EcoliWiki is a wiki-based system for finding, editing, and adding information about E. coli K-12 and other model organism strains of E. coli. EcoliWiki is being constructed to include information about bacteriophage, plasmids, and mobile genetic elements. Information should be easily accessible and correct, and users have the right to edit any information they feel is incorrect. Most of the E. coli information was initially seeded with a subset of information from parsing EcoCyc data dumps. For phage gamma and the F plasmid, Genbank accessions were converted to GFF, which was parsed into the appropriate tables. Other sources of content include: * user additions * monthly addition of annotations from EcoCyc * structural data from the PDB * domains and motif information from InterPro * various databases including EcoGene, RegulonDB, Genbank, GenoBase, ASAP * many many scientific papers EcoliWiki participates in the RefGenome project. EcoliWiki provides REST web services as part of the EcoliHub Web Services infrastructure project.

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Cite this (FuncAssociate: The Gene Set Functionator, RRID:SCR_005768)

URL: http://llama.mshri.on.ca/funcassociate/

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

A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool

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Cite this (GeneCodis, RRID:SCR_006943)

URL: http://genecodis.cnb.csic.es/

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

Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology.

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Cite this (Genevestigator, RRID:SCR_002358)

URL: https://www.genevestigator.com/gv/

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

A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools.

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Cite this (GREC Corpus, RRID:SCR_006719)

URL: http://www.nactem.ac.uk/GREC/

Resource Type: Resource, training set

A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format

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    gsGator

Cite this (gsGator, RRID:SCR_012035)

URL: http://gsgator.ewha.ac.kr/

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

A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks.

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Cite this (Information Hyperlinked Over Proteins, RRID:SCR_004829)

URL: http://www.ihop-net.org/UniPub/iHOP/

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

Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.

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