| Figure 1: Highly structured knowledge base by auto-clustering of co-herent content. Designing bio-molecular and bio-production projects generally needs evidence based information. This information is of high complexity and needs high level of structuring. We combine auto-cluster software tools with knowledge bases of different sources in order to get direct access to all project relevant data and information. (click image to enlarge) |
EvoMAG TM - Gene Developer Platform for Reverse Genetic Engineering and Design of Synthetic Biology Applications
Basic Package - Sequence Editor - Codon Table Editor for designing reduced codon tables - Internet Access to Codon Table Data Base - Secondary Structure Analysis - Restriction Analysis - Synonymous codon optimization by in silico mutagenesis genetic algorithms - GC- content standard deviation
Upgrade Package 1 : Statistic Codon optimization simultaneous with the feature secondary structure reduction
Upgrade Package 2 : Statistic codon optimization simultaneous with the feature "IN and OUT" - calculation of restriction sites
Upgrade Package 3 : Statistic codon optimization simultaneous with the features secondary structure reduction and "IN and OUT" - calculation of restriction sites
Full Package - Sequence Editor - Codon Table Editor for designing reduced codon tables - Internet Access to Codon Table Data Base - Secondary Structure Analysis - Restriction Analysis - Synonymous codon optimization by in silico mutagenesis genetic algorithms - Statistic codon optimization simultaneous with the features secondary structure reduction and "IN and OUT" - calculation of restriction sites
| Figure 2: Calculating the restriction sites. First all restriction sites are removed an calculate out of a protein coding sequence by simultaneous CAI-adaption optimization. Then a list of selected enzymes (e.g. all palindromic 6mers) is calculated by the program for make proposals where R-sites can be inserted without changing the protein sequence. Regions of interest (ROIs) can be defined. Modes of Fig. 2 and 3 can be combined to get more parameters optimized simultaneously. (click image to enlarge) |
| Figure 3: Calculating the secondary structures out of a zinc-finger protein by simultaneous CAI (codon adaption index) optimization. Blue and Red bars are indicating secondary structures which are calculated out of the gene variant population by mutations. All mutations are silent ones and do not affect integrity of the protein sequence (click image to enlarge) |