Hey there! Thank you for some amazing work. I'm interested in extending linearDesign to operate under constrains - in particular I would like to come up with structures that unite the two ends of the coding region. I can think of some ad-hoc ways of doing this by stitching together the output of linear design on various synthetic inputs ( for instance with a 300bp CDS, input the first 50 and last 50 bp of the amino acid sequence, with a spacer in the middle, use this encoding for that outer region, then repeat the process walking inwards to bp 50-100 and 200-250, until the middle is reached. Possibly using variable dynamic regions that place the window sizes at non structured base pairs), but this, I imagine, is going to give sub optimal results. Any thoughts on how one could extend the algorithm to work under constraints like this?
Hey there! Thank you for some amazing work. I'm interested in extending linearDesign to operate under constrains - in particular I would like to come up with structures that unite the two ends of the coding region. I can think of some ad-hoc ways of doing this by stitching together the output of linear design on various synthetic inputs ( for instance with a 300bp CDS, input the first 50 and last 50 bp of the amino acid sequence, with a spacer in the middle, use this encoding for that outer region, then repeat the process walking inwards to bp 50-100 and 200-250, until the middle is reached. Possibly using variable dynamic regions that place the window sizes at non structured base pairs), but this, I imagine, is going to give sub optimal results. Any thoughts on how one could extend the algorithm to work under constraints like this?