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Are you working in academia? It might be worthwhile to call the companies directly and see if there is a discounted rate for your institution (another lab or department may have already set something up). You won't be able to get information on the different algorithms if they are proprietary. However considering that codon usage data is public and shared ...


3

I read through the paper. The author starts by stating that as of the time of writing, two different classes of codon usage profiles were known (or at least putatively so). All 782 unique CDS sequences used were subjected to a two-step classification method. In step one, each CDSs was broken down into a 61-dimensional vector representing each of the 61 ...


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I have written a script that will get you started. It downloads all protein coding transcripts of the species of interest from Ensembl and prints the codon use for each codon on each transcript. You will need to install the Bio::EnsEMBL::Registry Perl module, see here for instructions. The script also uses the Math::Round module, everything else should be ...



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