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Links tagged with 'bacterial gene expression regulation'

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BioCyc Knowledge LibraryDatabase Content

http://www.biocyc.org/

Protein > Interactions, Pathways, Enzymes

BioCyc is a collection of pathway/genome databases derived either from the literature (EcoCyc and MetaCyc) or computationally (ie. HumanCyc). EcoCyc is used to visualize gene layout, biochemical reactions, and pathways for the E. coli chromosome; MetaCyc contains the enzymes, reactions, and pathways for a variety of organisms (mostly micro-organisms)

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tagsbacterial gene expression regulation bacterial genome database management systems enzymes escherichia coli escherichia coli proteins genetic databases genome humans metabolism protein databases protein transport signal transduction

EcoCycDatabase Content

http://EcoCyc.org

Model Organisms > Databases

EcoCyc is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in multiple ways. New features include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein activity.

NAR Database Issue 2011
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tagsbacterial gene expression regulation binding sites escherichia coli k12 escherichia coli proteins genetic databases genetic transcription signal transduction transcription factors

Pseudomonas Genome DatabaseDatabase Content

http://www.pseudomonas.com

Model Organisms > Databases

The Pseudomonas Genome Database integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions, experimental data, and manually curated, community-based annotation updates. Comparative genomics analyses incorporate robust genera-geared methods for predicting and clustering orthologs.

This content is being maintained by fionabrinkman.

NAR Database Issue 2011
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tagsbacterial dna bacterial gene expression regulation bacterial genes bacterial genome bacterial proteins computational biology dna sequence analysis genetic databases genetic polymorphism genomic islands genomics human genome humans microbial drug resistance molecular sequence data pseudomonas pseudomonas aeruginosa pseudomonas infections species specificity systems integration voluntary workers

Pseudomonas Genome ProjectDatabase Content

http://pseudomonas.com/

Model Organisms > Microbes

This is a comprehensive database on all Pseudomonas species genomes providing primarily access to Pseudomonas aeruginosa genomic data and annotation. Its interface faciliates comparative analyses of genes, proteins, annotations and gene orders, and contains a wealth of additional data including pathway-based, operon-based, protein-localization based, gene function category and ortholog/paralog-based information.

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tagsbacterial dna bacterial gene expression regulation bacterial genome bacterial proteins computational biology dna sequence analysis genetic databases genomics humans microbial drug resistance molecular sequence data pseudomonas aeruginosa pseudomonas infections species specificity systems integration

RegulonDBDatabase Content

http://regulondb.ccg.unam.mx/

Model Organisms > Databases

RegulonDB is a reference database of Escherichia coli K-12. Transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.

NAR Database Issue 2011
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tagsbacterial gene expression regulation binding sites escherichia coli k12 gene regulatory networks genetic databases genetic transcription signal transduction systems integration transcription factors transcription initiation site

RibExTool Content

http://www.ibt.unam.mx/biocomputo/RibEx.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Riboswitch Explorer (RibEx) searches sequences for known riboswitches and also for predicted bacterial regulatory elements that are highly conserved

NAR Web Server Issue 2005
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tagsbacterial gene expression regulation bacterial rna base sequence conserved sequence dna sequence analysis open reading frames ribonucleic acid regulatory sequences

RNApredatorTool Content

http://rna.tbi.univie.ac.at/RNApredator

Model Organisms > Microbes
RNA > Functional RNAs

RNApredator is a web server for the prediction of bacterial sRNA targets. The user can choose from a large selection of genomes. Accessibility of the target to the sRNA is considered.

NAR Web Server Issue 2011
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tagsbacterial gene expression regulation bacterial genome bacterial rna messenger rna rna sequence analysis small untranslated rna

WebGeSTer DBDatabase Content

http://pallab.serc.iisc.ernet.in/gester

DNA > Databases

WebGeSTer DB a database of intrinsic transcription terminators identified in bacterial genome sequences and plasmids. Users can obtain both graphic and tabular results on putative terminators based on default or user-defined parameters. The results are arranged in different tiers to facilitate retrieval, as per the specific requirements. An interactive map has been incorporated to visualize the distribution of terminators across the whole genome.

NAR Database Issue 2011
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tagsbacterial gene expression regulation bacterial genome genetic terminator regions nucleic acid databases