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XenoExpressO -- Xeno-sequence Expression Optimisation

No-frills web-service for the optimisation of expression vectors used in a prokaryotic translation system harboring coding sequences of eukaryotic origin.

Background: Prokaryotic and eukaryotic translation machinery are quite different. Consequently, their mRNA differ in various aspects. Nevertheless, it is common routine to express genes from an eukaryotic, e.g. human, origin in a bacterial system. Therefore, typically the gene is incorporated into an expression vector equipped with bacterial promoter and a 5'utr shown to be efficiently expressed by the prokaryotic translation machinery. Nonetheless, sometimes this constructs fail to produce significant amounts of protein. One potential cause are possible RNA structures formed at the ribosome binding site due to its new sequence context, namely the newly attached downstream coding sequence (cds). The XenoExpressO webserver allows its user to adapt a current expression construct in a way that 5'utr and cds match each other with respect to possible detrimental secondary RNA structures. To this end, the cds is modified without altering the amino acid seqeuence it codes for. The 5'utr itself is unchanged. A detailed description of the applied method can be found in this pre-print.

Usage: Simply type or paste the 5'utr and coding sequence of your expression construct in the appropriate field below and click Proceed. You can test the server using a provided example sequences, or directly inspect the result page of the example sequences.

Help: Further detailed description of the expected input for each input field is provided as a hover text if the mouse cursor is positioned over the respective field.

Required input data:

Paste or type your 5'UTR sequence
Paste or type your coding sequence

Notification via e-mail upon completion of the job (optional):  

Advanced parameter options:

Paste or type codon sequences which should be avoided to be introduced. Each line is considered as one codon.
Paste or type sequence motifs which should be avoided to be introduced (e.g., restriction enzyme recognition motifs). Each line is considered as one motif.