This algorithm determines the Shine-Dalgarno (SD) and Anti-Shine-Dalgarno (ASD) sequences for development of orthogonal ribosomes.
Steps 6 and 7 Details
Take the output from step 4-5. Predict the secondary structure of all candidate ribosomes and discard those that form any kind of hairpin structure within the ASD region.
Responsible functions: RNAfoldcentroidseq, secstructurelib, ASD_2rystructure_narrow
Function description: RNAfoldcentroidseq
This function takes in a sequence as an input, then makes use of the program RNAfold to predict the most probably secondary structure resulting from the primary structure. The option using centroid ensemble is shown to be more reliable compared to the default option
[2]. The output is a bracket/dot form of the sequence that indicates whether each base is part of any secondary structure.
Function description: secstructurelib
This function takes in a library of sequences of ASD and SD, put each ASD in the corresponding position in the 16s rRNA, and use RNAfoldcentroidseq to return a library that contains all the secondary structures of all candidate 16s rRNAs.
Function description: ASD_2rystructure_narrow
This function takes in a library, run the library through secstructurelib to get a representative library of secondary structure, and filter out those with secondary structures in the ASD region. The whole pipelines of processing the input library is shown in the figure below.
Figure S4. Elimination of sequences that lead to secondary structure complications.
