Consequences of partial CDS optimization

[i-hate-this-username]

Hi there,

If this isn't the right place to ask, please let me know!

In our lab, we're utilizing a library of modules for the N and C terminals because they are repetitive for our experiments. This helps us save on the everyday generation of oligos. Consequently, we don't typically need to optimize the entire coding sequence; we focus primarily on the central part, keeping the terminal sections (50-100 bp) unchanged, and therefore "finalize" the plasmid and the whole protein sequence during the Golden Gate assembly.

Here's my question: When we use the "AvoidChanges" constraint for these terminal parts that are the parts of the protein sequence, could it potentially impact the optimization process?

For example, suppose we have a coding sequence of 1000 bp (positioned from 0 to 1000) with constraints to avoid changes from positions 0 to 100 and 900 to 1000. Should we consider adding any other parameters specific to this kind of optimization constraint?

Thanks!