Wolfram Mathematica

String Decomposition

Examine the relative frequencies of codons (groups of three consecutive nucleotides) in the list of nucleotides of a gene.

Get the DNA sequence of the human gene "SCNN1A".

In:= dnasequence = GenomeData["SCNN1A", "FullSequence"];

Use StringPartition to construct the corresponding list of codons.

In:= codons = StringPartition[dnasequence, 3];
In:= Take[codons, 10]
Out= Compute the relative frequency of each codon in this gene.

In:= frequencies = N[Counts[codons]/Length[codons]];

There are 64 possible codons formed from the A, C, G, T nucleotides, and they all appear in the gene chosen.

In:= frequencies // Length
Out= Find the three codons with the highest frequencies.

In:= TakeLargest[frequencies, 3]
Out= Find the three codons with the lowest frequencies.

In:= TakeSmallest[frequencies, 3]
Out= Visualize all relative frequencies in a Grid.

show complete Wolfram Language input
In:= background = Thread[Rule[ Flatten[{ Outer[List, Range[1, 15, 2], {3, 4, 7, 8}], Outer[List, Range[2, 16, 2], {1, 2, 5, 6}] }, 2], GrayLevel[0.9]]]; Grid[Partition[Sequence @@@ Normal[KeySort@frequencies], 8], Spacings -> {1, 1}, Dividers -> All, Background -> {None, None, background}]
Out= 