Bioinformatics Toolbox™

dimercount - Count dimers in nucleotide sequence

Syntax

Dimers = dimercount(SeqNT) [Dimers, Percent] = dimercount(SeqNT) ... = dimercount(SeqNT, 'Chart', ChartValue)

Arguments

SeqNT

One of the following:

String of codes specifying a nucleotide sequence. For valid letter codes, see the table Mapping Nucleotide Letter Codes to Integers.
Row vector of integers specifying a nucleotide sequence. For valid integers, see the table Mapping Nucleotide Integers to Letter Codes.
MATLAB^® structure containing a Sequence field that contains a nucleotide sequence, such as returned by fastaread, emblread, getembl, genbankread, or getgenbank.

Examples: 'ACGT' or [1 2 3 4]

ChartValue String specifying a chart type. Choices are 'pie' or 'bar'.

Return Values

`Dimers`	MATLAB structure containing the fields `AA`, `AC`, `AG`, `AT`, `CA`, `CC`, `CG`, `CT`, `GA`, `GC`, `GG`, `GT`, `TA`, `TC`, `TG`, and `TT`, which contain the dimer counts in `SeqNT`.
`Percent`	A 4-by-4 matrix with the relative proportions of the dimers in `SeqNT`. The rows correspond to `A`, `C`, `G`, and `T` in the first element of the dimer, and the columns correspond to `A`, `C`, `G`, and `T` in the second element of the dimer.

Description

Dimers = dimercount(SeqNT) counts the nucleotide dimers in SeqNT, a nucleotide sequence, and returns the dimer counts in Dimers, a MATLAB structure containing the fields AA, AC, AG, AT, CA, CC, CG, CT, GA, GC, GG, GT, TA, TC, TG, and TT.

For sequences that have dimers with the character U, these dimers are added to the corresponding dimers containing a T.
If the sequence contains ambiguous nucleotide characters (R, Y, K, M, S, W, B, D, H, V, or N), or gaps indicated by a hyphen (-), then these characters are counted in the field Others, and the following warning message appears.
```
Warning: Ambiguous symbols appear in the sequence. These will be in Others.
```
If the sequence contains undefined nucleotide characters (E, F, H, I, J, L, O, P, Q, X, or Z), then dimers containing these characters are counted in the field Others, and the following warning message appears:
```
Warning: Unknown symbols appear in the sequence. These will be in Others.
```

[Dimers, Percent] = dimercount(SeqNT) returns Percent, a 4-by-4 matrix with the relative proportions of the dimers in SeqNT. The rows correspond to A, C, G, and T in the first element of the dimer, and the columns correspond to A, C, G, and T in the second element of the dimer.

... = dimercount(SeqNT, 'Chart', ChartValue) creates a chart showing the relative proportions of the dimers. ChartValue can be 'pie' or 'bar'.

Examples

Count the dimers in a nucleotide sequence and display a matrix of the percentage of each dimer.