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3.4 years ago
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How to customize the values assigned to nucleotides A, T, C, G in Codonw? And the equation?
Equation 1
code = ((P1 - 1)*16) + P2 + ((P3-1)*4)
For example, in the equation I would like to change P2 by P3.
nucleotides
T/U=1, C=2, A=3, G=4.
T = 1 would like to change to T = 2
What I found so far was:
http://codonw.sourceforge.net/DataRecoding.html
To aid computation codonW converts sequence information automatically from its original text format into a numerical format. This is normally transparent to the user. To add additional genetic codes or a personal choice of codon values for calculating the Fop, CAI or CBI indices, some understanding of the scheme used to convert the sequences to numerical strings is advisable.
When calculating the indices Fop, CBI, or CAI which are a measure of codon bias in relation to the codon usage of a set of optimal genes, there is an option of using a personal choice of these values. These are read from file, there must be one value for each codon (64 in total) and they must be found in the file in a set sequence (i.e. the numerical order of the codons, TTT, TCT ... GAG, GGG). This is also the order in which codon and amino acid results are recorded to file.
https://pypi.org/project/codonw-slim/
The genetic codes can be specified by setting the CodonSeq.genetic_code property with a pd.Series whose index is a codon and value is the single letter amino acid. Instantiate an object and see CodonSeq.genetic_code for more details.
I do not know how to do. I work on the Ubuntu -WSL terminal. I can't find information on how to do this. can you help me? How to make this kind of change? how to customize the equation and nucleotide values?
