Welcome to the Evolutionary Failure Mode (EFM) Optimizer! We hope that using our product, you will be able to easily design synthetic sequences with higher stability and expression level.
Our product is contained in the Optimizer directory. Sample input and output data, and code, are placed in the respective directories.
Our basic service will allow you to easily find and rank simple sequence repeats (SSR) and repeat mediated deletions (RMD) sites, for many files at once. These are mutational hotspots, which reduce genetic stability significantly.
In the case of mammalian or insectoid cells, methylation sites become significant factors in the host’s stability, as they are epigenetic inheritance hotspots. For these cells, we offer the ability to find methylation sites as well.
Finally, we believe that working with a list of problematic sites is inconvenient. We offer a further service of optimizing the input sequence. It is optimized for avoidance of these sites, preservation of GC content specified by the user, and codon usage.
In essence, you will provide input genetic sequences, and receive an equivalent sequence, optimized for stability and expression level. At the end of the optimization process, the software will produce a zip report including the annotated final sequence with the marked changes, and csv files that lists the successful constraints and objectives.
For the theoretical background, please refer to the documentation in our website: https://2020.igem.org/Team:TAU_Israel/Contribution. For questions and suggestions, contact the developers at: igem.tau.2019@gmail.com and mention in the title "EFM Optimizer V1".