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PRODORIC Release 8.9Prokaryotic database of gene regulation and systems biology
http://www.prodoric.de/
Prokaryotic database of gene regulation and systems biology
http://www.prodoric.de/
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PRODORIC Release 8.9 | prodoric.de Reviews
https://prodoric.de
Prokaryotic database of gene regulation and systems biology
prodoric.de
PRODORIC Release 8.9
http://www.prodoric.de/index.php?index=2
Query Database - Brief Introduction. Step 1 - Select Query Form. Select a query form from the menu or click on the image. The following forms and information contents are provided:. Gene and operon structure, genomic context, codon usage, GC content. Amino acid sequence, structural and functional information, interactions with other proteins and DNA binding sites. Information about DNA bindings sites of transcriptional regulators, sequence, genomic context, mode of interaction.
PRODORIC Release 8.9
http://www.prodoric.de/index.php?index=1
Welcome to the PRODORIC. Is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites. A variety of bioinformatics tools for the prediction, analysis and visualization of regulons and gene reglulatory networks is included. Click here to query the database. Please cite PRODORIC and results obtained by the use of the database as:. PRODORIC: prokaryotic database of gene regulation.
GBpro Genome Browser V.3.0
http://www.prodoric.de/gbpro.php
GBpro Genome Browser V.3.0. Acaryochloris marina (strain MBIC 11017) complete chromosome. Acaryochloris marina (strain MBIC 11017) complete chromosome. Acaryochloris marina (strain MBIC 11017) complete chromosome. Acaryochloris marina (strain MBIC 11017) complete chromosome. Acaryochloris marina (strain MBIC 11017) complete chromosome. Acaryochloris marina (strain MBIC 11017) complete chromosome. Acaryochloris marina (strain MBIC 11017) complete chromosome. Acholeplasma laidlawii (strain PG-8A). Acinetob...
PRODORIC Release 8.9
http://www.prodoric.de/statistics.php
Number of annotated publications:. Number of available genomes:. Aeropyrum pernix (strain K1). Agrobacterium tumefaciens (strain C58 / ATCC 33970 / ATCC 33970 [Dupont]). Bacillus subtilis (strain 168). Bradyrhizobium japonicum (strain USDA 110). Corynebacterium glutamicum (strain DSM 20300 / ATCC 13032 / NCIB 10025 [Kalinowski]). Escherichia coli O6 (strain UPEC / O6:H1 / ATCC 700928 / CFT073). Escherichia coli (strain K12). Escherichia coli (strain Sakai / O157:H7 / RIMD 0509952 / EHEC). Yersinia pseudo...
Virtual Footprint - bacterial regulon analyzer - main page
http://www.prodoric.de/vfp
Virtual Footprint is a new software suite for recognizing single or composite DNA patterns. It was especially designed to analyze transcription factor binding sites in whole bacterial genomes and their underlying regulatory networks. A pattern can consist of up to two subpatterns separated by a variable spacer region. Virtual Footprint can deal with three types of subpatterns: Position Weight Matrices, IUPAC Code and Regular Expressions. There are two types of analyses available:.
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JCat: A novel tool to adapt codon usage of a target gene to its potential expression host.
http://www.jcat.de/Start.jsp
Bioinformatic tools from our team:. JCat was published in NAR. 1 Type/paste sequences below:. Standard genetic code is used for the input sequence. Click here. 2 Specify the pasted Sequence:. Eukaryotes - - - - - - - - - - - -. Aspergillus niger ATCC 1015. Aspergillus niger NRRL 3. Prokaryotes - - - - - - - - - - - -. Acidobacteria bacterium (strain Ellin345). Acinetobacter sp. (strain ADP1). Aeropyrum pernix (strain K1). Agrobacterium tumefaciens (strain C58 / ATCC 33970 / ATCC 33970 [Cereon]). Bacillus...
ProdoNet
http://prodonet.tu-bs.de/query.php
Ensp; PRODORIC. Please enter your gene or protein identifiers/names:. Example for Pseudomonas aeruginosa. Example for Escherichia coli. Bacillus anthracis str. Ames. Bacillus cytotoxicus NVH 391-98. Bacillus licheniformis ATCC 14580. Bacillus subtilis subsp. subtilis str. 168. Bacillus thuringiensis serovar konkukian str. 97-27. Citrobacter koseri ATCC BAA-895. Cronobacter sakazakii ATCC BAA-894. Enterobacter sp. 638. Escherichia coli str. K-12 substr. MG1655. Pseudomonas syringae pv. syringae B728a.
JCat: A novel tool to adapt codon usage of a target gene to its potential expression host.
http://www.jcat.de/ChangeTranslation.jsp
Bioinformatic tools from our team:. JCat was published in NAR. Change applied code for translation. Genetic code used for the input sequence (Default: Standard genetic code):. Translation Input Sequence - - - - - - - - - - - -. Mold Mitochondrial; Protozoan Mitochondrial; Coele. Ciliate Nuclear; Dasycladacean Nuclear; Hexamita N. Echinoderm Mitochondrial; Flatworm Mitochondrial. Bacterial and Plant Plastid. 2004-2008 by Andreas Grote • andreas.grote@tu-bs.de.
JCat: A novel tool to adapt codon usage of a target gene to its potential expression host.
http://www.jcat.de/CAICalculation.jsp
Bioinformatic tools from our team:. JCat was published in NAR. 1 Upload Fasta File:. 2 Select the organism:. Eukaryotes - - - - - - - - - - - -. Aspergillus niger ATCC 1015. Aspergillus niger NRRL 3. Prokaryotes - - - - - - - - - - - -. Acidobacteria bacterium (strain Ellin345). Acinetobacter sp. (strain ADP1). Aeropyrum pernix (strain K1). Agrobacterium tumefaciens (strain C58 / ATCC 33970 / ATCC 33970 [Cereon]). Agrobacterium tumefaciens (strain C58 / ATCC 33970 / ATCC 33970 [Dupont]). Bacillus thuring...
JCat: A novel tool to adapt codon usage of a target gene to its potential expression host.
http://www.jcat.de/Literature.jsp
Bioinformatic tools from our team:. JCat was published in NAR. Grote A, Hiller K, Scheer M, Munch R, Nortemann B, Hempel DC, Jahn D. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W526-31. Sharp PM, Li WH. Codon usage in regulatory genes in Escherichia coli. Does not reflect selection for 'rare' codons. Nucleic Acids Res. 1986 Oct 10;14(19):7737-49. Sharp PM, Li WH. Carafa YA, Brody E, Thermes C. Limitations of...
JCat: A novel tool to adapt codon usage of a target gene to its potential expression host.
http://www.jcat.de/Download.jsp
Bioinformatic tools from our team:. JCat was published in NAR. It is strongly recommended to use the jar-file. This version of JCat is the most advanced and runs under all sytems. Updated jar-File works now under all systems! This version requires Java 1.5 or higher. Instructions for the jar-File:. 1 Open shell or terminal. 2 Type: "java -jar jcat.jar". Application: jcat.tar.gz. Install instructions for the Linux-application:. 1 Unpack the package. Install instructions for the Windows-application:.
JCat: A novel tool to adapt codon usage of a target gene to its potential expression host.
http://www.jcat.de/Introduction.jsp
Bioinformatic tools from our team:. JCat was published in NAR. The CodonAdaptationTool (JCAT) presents a simple method to adapt the Codon Usage to most sequenced prokaryotic organisms and selected eukaryotic organisms. The codon adaptation plays a major role in cases where foreign genes are expressed in hosts and the codon usage of the host differs from that of the organism where the gene stems from. Unadapted codons in the host can for example lead to a minor expression rate.
JCat: A novel tool to adapt codon usage of a target gene to its potential expression host.
http://www.jcat.de/Screenshots.jsp
Bioinformatic tools from our team:. JCat was published in NAR. In this example the CodonUsage of the gene 'anr' from Pseudomonas aeruginosa. Was adapted to Bacillus subtilis. The first screenshot shows the Codon Usage in B. subtilis. Before the codon Adaptation:. The red line shows the Codon Usage for each codon present in the gene. The blue line depicts the mean Codon Usage in B. subtilis. The second screenshot shows the adapted Codon Usage for this gene in B. subtilis.
JCat: A novel tool to adapt codon usage of a target gene to its potential expression host.
http://www.jcat.de/Links.jsp
Bioinformatic tools from our team:. JCat was published in NAR. PRODORIC - Prokaryotic Database of Gene Regulation and Regulatory Networks. JVirGel - Virtual 2D-protein gels. PrediSi - PREDIction of SIgnal peptides. REBASE - The Restriction Enzyme Database. TransTerm - Transcription Terminators in bacterial genomes. 2004-2008 by Andreas Grote • andreas.grote@tu-bs.de.
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PRODORIC Release 8.9
Welcome to the PRODORIC. Is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites. A variety of bioinformatics tools for the prediction, analysis and visualization of regulons and gene reglulatory networks is included. Click here to query the database. Please cite PRODORIC and results obtained by the use of the database as:. PRODORIC: prokaryotic database of gene regulation.
PRODORIC Release 8.9
Welcome to the PRODORIC. Is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites. A variety of bioinformatics tools for the prediction, analysis and visualization of regulons and gene reglulatory networks is included. Click here to query the database. Please cite PRODORIC and results obtained by the use of the database as:. PRODORIC: prokaryotic database of gene regulation.
PRODORIC Release 8.9
Welcome to the PRODORIC. Is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites. A variety of bioinformatics tools for the prediction, analysis and visualization of regulons and gene reglulatory networks is included. Click here to query the database. Please cite PRODORIC and results obtained by the use of the database as:. PRODORIC: prokaryotic database of gene regulation.
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