As a pilot experiment we did CLIP (to find RNA bound to protein) and BONCAT (to find which proteins have reduced translation) in cells over-expressing my protein of interest. Turns out, my protein binds to specific tRNAs and seemingly reduces translation of a specific subset of proteins when it accumulates as in disease conditions. So, I'm trying to see if proteins that have lowered translation have an overabundance of the amino acids corresponding to the tRNAs bound to my protein. Theoretically, maybe my protein is reducing translation by sequestering those tRNA and making the ribosome stall while waiting for the proper tRNA to come by during translation.
I've taken all of the cDNA sequences of the proteins I'm interested in, but I'm not sure exactly how to proceed and do this sort of analysis. I've looked up various codon bias packages, but I can't seem to get the older ones (codonO, codonW) working, and the newer ones go far beyond what I think I need (coRdon).
Am I just overthinking this? Can I simply find the measure of the codon usages by looping through my multifasta file, counting codon by codon, and then normalize to sequence by dividing each gene's count by that gene's sequence length?
My lab doesn't normally work with any bioinformatics, we just do wet lab science, so any suggestions are greatly appreciated. Thanks.