Hello!
I've recently become involved in undergraduate research. Our research concerns the level of expression of H protein in canine distemper virus and measles virus (right now at least). It involves codon usage bias in these organisms in different cell types and species and we've received interesting data involving expression levels after global optimization and sub-optimizations of the H protein. What I want to do is narrow down the areas in these sequences that are the most important in producing the expression patterns we've seen but I've been having trouble finding databases/literature that are relevant. I'm just looking to be pointed in the right direction since I'm new to this and still have a lot to learn. Thanks!
Edit:
What's relevant to me is our data regarding DNA constructs transfected into human (293 HEK) cells (I'll ignore our data on canine cells here for the sake of simplicity). Regulatory elements here can be disregarded in our constructs and I'm strictly concerned with codon optimization and sub-optimization of the protein coding region. So think of it this way: global (sub-)optimization of the codons for host cell machinery resulted in vastly increased protein production, even when sub-optimized. I want to know which parts of this coding region are likely to be most relevant in expression, so that these regions can be exclusively selected for optimization treatments and further analysis.
It's not really clear what you're looking for.
What kind of sequences in what kinds of organisms?
What's relevant to me is our data regarding DNA constructs transfected into human (293 HEK) cells (I'll ignore our data on canine cells here for the sake of simplicity). Regulatory elements here can be disregarded in our constructs and I'm strictly concerned with codon optimization and sub-optimization of the protein coding region. So think of it this way: global (sub-)optimization of the codons for host cell machinery resulted in vastly increased protein production, even when sub-optimized. I want to know which parts of this coding region are likely to be most relevant in expression, so that these regions can be exclusively selected for optimization treatments and further analysis. To decide on which regions are important, I would like data on expression patterns that are relevant here but my issue is that I'm having trouble finding or even knowing where to find relevant data. I appreciate your reply though, thank you.