Determining Codon Composition :: Sequence Analysis (Bioinformatics Toolbox)

Bioinformatics Toolbox

Determining Codon Composition

Trinucleotides (codon) code for an amino acid, and there are 64 possible codons in a nucleotide sequence. Knowing the percent of codons in your sequence can be helpful when you are comparing with tables for expected codon usage.

After you read a sequence into MATLAB, you can analyze the sequence for codon composition. This procedure uses the human mitochondria genome as an example. See Getting Sequence Information into MATLAB.

Count codons in a nucleotide sequence. In the MATLAB Command Window, type

codoncount(mitochondria)

MATLAB displays the codon counts for the first reading frame.

AAA-172  AAC-157  AAG-67  AAT-123
ACA-153  ACC-163  ACG-42  ACT-130
AGA-58   AGC-90   AGG-50  AGT-43
ATA-132  ATC-103  ATG-57  ATT-96
CAA-166  CAC-167  CAG-68  CAT-135
CCA-146  CCC-215  CCG-50  CCT-182
CGA-33   CGC-60   CGG-18  CGT-20
CTA-187  CTC-126  CTG-52  CTT-98
GAA-68   GAC-62   GAG-47  GAT-39
GCA-67   GCC-87   GCG-23  GCT-61
GGA-53   GGC-61   GGG-23  GGT-25
GTA-61   GTC-49   GTG-26  GTT-36
TAA-136  TAC-127  TAG-82  TAT-107
TCA-143  TCC-126  TCG-37  TCT-103
TGA-64   TGC-35   TGG-27  TGT-25
TTA-115  TTC-113  TTG-37  TTT-99

Count the codons in all six reading frames and plot the results in a heat map.

for frame = 1:3
    figure('color',[1 1 1])
    subplot(2,1,1);
    codoncount(mitochondria,'frame',frame,'figure',true);
    title(sprintf('Codons for frame %d',frame));     
    subplot(2,1,2);     
    codoncount(mitochondria,'reverse',true,
                            'frame',frame,
                            'figure',true);     
    title(sprintf('Codons for reverse frame %d',frame)); 
end

MATLAB draws heat maps to visualize all 64 codons in the six reading frames.

Determining Nucleotide Composition

Open Reading Frames