Virtual Footprint is a new sensitive search tool 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 various subpatterns separated by a variable spacer region, however this web version is restricted to bipartite patterns due to the time consuming calculation process. The definition of a subpattern is realized either by a position weigth matrix or a IUPAC consensus or a regular expression. A huge library of bacterial position weight matrices is provided.
Furthermore the programm offers the possibility of analzing the results according to their genomic context. Matches in coding regions can be excluded, the size of the upstream region (distance to the start codon) can be defined and the pattern orientation can be selected. The result is a list of potential binding sites and corresponding genes defining the whole regulon. All matches are hyperlinked to an interactive genome browser to get a visialization of the genomic region and genes are linked to the PRODORIC database to provide further information about the molecular networks.

http://www.prodoric.de/vfp

GBpro is a genome browser for an interactive navigation through all bacterial genomes available in PRODORIC. Genes, promoters and binding sites are displayed in parallel as graphical map and highlighted sequence. Optionally the GC content and stacking energie can be visualized. All results of Virtual Footprint are directly linked to GBpro and can thereby be visualized in their genomic context. Similarly genes and transcription factor binding sites present in PRODORIC are directly linked this genome browser.

http://www.prodoric.de/gbpro.php

JVirGel is a software for the simulation and analysis of proteomics data [1]. The JavaTM based software determines the theoretical isoelectric points (pI) and the calculated molecular weights (MW) of proteins and visualizes these as a virtual two-dimensional (2D) protein map. The user is able to control the presentation of the calculated 2D gel interactively by selecting a pI/MW range and an electrophoretic timescale of interest.

• Standalone application:
  This version needs to be installed on the user's computer. However, this version offers the most advanced features. Currently, the application resides in a beta stadium and will be available at spring/summer 2004. If you would like to become a beta tester fell free to contact us.
• Java Applet:
  To run this version you need to have an installed Java Runtime Environment on your system. Due to the fact that applets are transferred via the internet they should be small-sized, thus the functional range of the applet is limited. Even though the applet offers the possibility to visualize 2D gels interactively. The applet can either import predefined data from the public database PRODORIC [2] or user-defined amino acid sequences in FASTA format. To start the applet click here.
• HTML-Version:
  This is an alternative for those who have not the possibility to run an Java applet. The only condition to run this version is an installed webbrowser. However the functionality of this version is very limited. Click here to start this version and select HTML-version in the menu of the next page.

http://www.jvirgel.de

• Field of Application
  It is especially useful for the fast analysis of large datasets because calculation is performed in real time with a high accuracy. Therefore PrediSi is well suited for the evaluation of whole proteome datasets which are currently accumulating during numerous genome projects and proteomics experiments.
• Method
  The employed method is based on a position weight matrix approach which is improved by a frequency correction that takes the amino acid bias present in proteins in consideration. The software was trained using sequences extracted from the most recent version of the SwissProt database.
• Availability
  PrediSi is freely accessible via web interface for the analysis of an unlimited number of sequences. Furthermore it can be download as a Java package and thus can be easily integrated into other software projects.

http://www.predisi.de

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. The adaptation is based on CAI-values proposed by PM Sharp et.al. The CAI-values were calculated by applying an algorithm from A Carbone et. al. The eukaryotic genomes of mouse and human contain different kinds of biases along the chromosomes and the algorithm is not perfectly suited for this problem. Results in this field should be handled with care. The mean codon usage for a certain organism was derrived by summing over all CAI-values of all genes of this organism (except genes without an amino acid sequence, e.g. RNAs) devided by the number of genes. This data is also presented in the graphical output of the codon adaptation. As a further option for the codon adaptation the opportunity to avoid rho-independent trancription terminators is provided. The algorithm for the prediction of these structures is based on a model from MD Ermolaeva et. al. For more details see the literature section. Another feature is the possibility to avoid restriction enzyme binding sites in the adapted DNA. The data for the restriction enzymes was therefor derrived from the "The Restriction Enzyme Database" (REBASE).

http://www.jcat.de