Paste the sequence information of the protein or gene of your interest in the input mask.
Choose the number of modified sequences to be generated.
Select a pre-trained profile for the adaptation to a model organism and press Generate.
Paste your protein or gene sequence of interest input field or choose one the example data sequences.
Select the number of sequences to generate.
Select one expression system profile out of the prepared list and press 'Generate'.
Filter resulting synonymous gene sequences for certain restriction sites or RNA stability levels (MFE).
Dynamically create a custom profile with alternative codon-usage weighting or by restricting the host genome data to protein subsets with specified abundancies or functional classes.
Set filter for resulting synonymous gene sequences based on restriction sites or RNA stability levels.
Restriction sites (all, commercial) to filter for, can be selected from a list or searched by their name and cleavage site pattern as termed in the REBASE database.
Synonymous sequences can be filtered by RNA stability levels by setting a certain MFE threshold. The RNAfold calculation is by default activated and results in longer computation times.
Based on the above selected expression system, custom profiles can be generated to produce synonymous sequences.
Customizing the profile can be achieved by selecting sets of the most frequent proteins.
Customizing the profile can be achieved by selecting proteins from specific classes like 'membrane' associated proteins. Multiple choices are here possible.
Customizing the profile can be achieved by selecting restricting the range of abundant proteins (from low frequent to high frequent proteins, based on PaxDB data).
Compare DNA sequence suggestions by functional alignments (plain, amino acids, codon differences).
Inspect single gene information such as sequence statistics, RNA stability and structure or base pairing sites.
Control the profile information of the model and the suggested genes (codon-usage heatmaps and tables).
Inspect the resulting synonymous sequences in multiple sequence alignments highlighted by aminoacid types or codon differences.
Inspect a single gene in detail by its key sequence information and RNAfold structure predictions.
Inspect a single gene in detail by its sequence codon usage or base pairing sites as predicted by RNAfold.
Inspect and compare the codon usages, di-codon-usage heatmaps, of the model and the resulting gene suggestions.
Inspect and compare the codon usages of the model and the resulting gene suggestions.
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