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Links tagged with 'operon'

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BROPResource Content

http://brop.org/

Expression > Transcript Expression Analysis
Model Organisms > Microbes

The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.

NAR Web Server Issue 2005
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tagsbacteria bacterial capsules bacterial genes bacterial genome bacterial polysaccharides bacterial proteins biological evolution computational biology dna transposable elements fungal genome genetic databases genetic variation genomic islands genomics horizontal gene transfer integrases mouth oligonucleotide array sequence analysis open reading frames operon porphyromonas gingivalis sequence alignment streptococcus mutans transfer rna virulence virulence factors

iCRTool Content

http://210.212.215.199/icr/index.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Interactions, Pathways, Enzymes

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.

NAR Web Server Issue 2006
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tags5' flanking region bacterial genome bacterial proteins binding sites dna-binding proteins genomics mycobacterium tuberculosis nucleic acid regulatory sequences operon prokaryotic cells regulon sequence alignment serine endopeptidases transcription factors transcriptional regulatory elements

ODBDatabase Content

http://operondb.jp/

DNA > Databases

ODB (Operon DataBase) contains all known and conserved operons in completely sequenced genomes.

NAR Database Issue 2011
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tagsgenomics nucleic acid databases operon

PredictRegulonTool Content

http://www.cdfd.org.in/predictregulon/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes.

NAR Web Server Issue 2004
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tags5' flanking region bacterial genome bacterial proteins binding sites mycobacterium tuberculosis nucleic acid regulatory sequences operon prokaryotic cells regulon sequence alignment serine endopeptidases transcription factors

ProdoNetTool Content

http://www.prodonet.tu-bs.de

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Microbes

A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.

NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial proteins gene expression profiling gene regulatory networks membrane proteins metabolic networks and pathways operon pseudomonas aeruginosa regulon

RegPreciseDatabase Content

http://regprecise.lbl.gov

DNA > Databases
Model Organisms > Databases

The RegPrecise database was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. The reconstructed regulons include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. Another section in the database represents the results of accurate regulon propagation to the closely related genomes.

NAR Database Issue 2010
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tagsalgorithms amino acid motifs bacterial genome binding sites computational biology dna genetic databases nucleic acid databases operon protein databases sequence alignment transcription factors

RegPredictTool Content

http://regpredict.lbl.gov

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

RegPredict web server provides comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics.

NAR Web Server Issue 2010
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tagsbacterial genome genomics operon regulon staphylococcaceae systems integration