Determining Nucleotide Composition :: Sequence Analysis (Bioinformatics Toolbox)

Bioinformatics Toolbox

Determining Nucleotide Composition

Sections of a DNA sequence with a high percent of A+T nucleotides usually indicates intergenic parts of the sequence, while low A+T and higher G+C nucleotide percentages indicate possible genes. Many times high CG dinucleotide content is located before a gene.

After you read a sequence into MATLAB, you can use the sequence statistics functions to determine if your sequence has the characteristics of a protein-coding region. This procedure uses the human mitochondrial genome as an example. See Getting Sequence Information into MATLAB.

Plot monomer densities and combined monomer densities in a graph. In the MATLAB Command window, type
```
ntdensity(mitochondria)
```
This graph shows that the genome is A+T rich.
Count the nucleotides using the function basecount.
```
basecount(mitochondria)
```
A list of nucleotide counts is shown for the 5'-3' strand.
```
ans = 
    A: 5113
    C: 5192
    G: 2180
    T: 4086
```
Count the nucleotides in the reverse complement of a sequence using the function seqrcomplement.
```
basecount(seqrcomplement(mitochondria))
```
As expected, the nucleotide counts on the reverse complement strand are complementary to the 5'-3' strand.
```
ans = 
    A: 4086
    C: 2180
    G: 5192
    T: 5113
```
Use the function basecount with the chart option to visualize the nucleotide distribution.
```
basecount(mitochondria,'chart','pie');
```
MATLAB draws a pie chart in a figure window.
Count the dimers in a sequence and display the information in a bar chart.
```
dimercount(mitochondria,'chart','bar')
```
MATLAB lists the dimer counts and draws a bar chart.

Getting Sequence Information into MATLAB

Determining Codon Composition