Bioinformatics Toolbox™

aacount - Count amino acids in sequence

Syntax

AAStruct = aacount(SeqAA) AAStruct = aacount(SeqAA, ...'Chart', ChartValue, ...) AAStruct = aacount(SeqAA, ...'Others', OthersValue, ...) AAStruct = aacount(SeqAA, ...'Structure', StructureValue, ...)

Arguments

`SeqAA`	One of the following: String of single-letter codes specifying an amino acid sequence. For valid letter codes, see the table Mapping Amino Acid Letter Codes to Integers. Unknown characters are mapped to `0`. Row vector of integers specifying an amino acid sequence. For valid integers, see the table Mapping Amino Acid Integers to Letter Codes. MATLAB structure containing a `Sequence` field that contains an amino acid sequence, such as returned by `fastaread`, `getgenpept`, `genpeptread`, `getpdb`, or `pdbread`. Examples: `'ARN'` or `[1 2 3]`
`ChartValue`	String specifying a chart type. Choices are `'pie'` or `'bar'`.
`OthersValue`	String specifying how to count ambiguous characters (`B`, `Z`, `X`), the stop character (`*`), and gaps indicated by a hyphen (`-`). Choices are `'full'` (lists the ambiguous characters in separate fields) or `'bundle'` (lists the ambiguous characters together in the field `Others`). Default is `'bundle'`.
`StructureValue`	Suppresses the unknown characters warning when set to `'full'` .

Return Values

AAStruct 1-by-1 MATLAB structure containing fields for the standard 20 amino acids (A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, and V).

Description

AAStruct = aacount(SeqAA) counts the number of each type of amino acid in SeqAA, an amino acid sequence, and returns the counts in AAStruct, a 1-by-1 MATLAB structure containing fields for the standard 20 amino acids (A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, and V).

If a sequence contains ambiguous characters (B, Z, or X), the stop character (*), or gaps indicated with 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 a sequence contains characters other than the 20 standard amino acids, ambiguous, stop, and gap characters, then 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.
```

If the property 'Others' is set to 'full', ambiguous characters are listed separately in the fields B, Z, X, Stop, and Gap.

AAStruct = aacount(SeqAA, ...'PropertyName', PropertyValue, ...) calls aacount with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

AAStruct = aacount(SeqAA, ...'Chart', ChartValue, ...) creates a chart showing the relative proportions of the amino acids. ChartValue can be 'pie' or 'bar'.

AAStruct = aacount(SeqAA, ...'Others', OthersValue, ...) specifies how to count ambiguous characters (B, Z, or X), the stop character (*), and gaps indicated by a hyphen (-). Choices are 'full' (lists the ambiguous characters in separate fields) or 'bundle' (lists the ambiguous characters together in the field Others). Default is 'bundle'.

AAStruct = aacount(SeqAA, ...'Structure', StructureValue, ...) suppresses the unknown characters warning when StructureValue is set to 'full'.

aacount(SeqAA) — Displays fields for 20 amino acids, and, if there are ambiguous or unknown characters, adds an Others field with the ambiguous and unknown character counts.
aacount(SeqAA, 'Others', 'full') — Displays fields for 20 amino acids, 3 ambiguous amino acids, stops, gaps, and, if there are unknown characters, adds an Others field with the unknown counts.
aacount(SeqAA, 'Structure', 'full') — Displays fields for 20 amino acids and an Others field. If there are ambiguous or unknown characters, adds the counts to the Others field; otherwise displays 0 in the Others field.
aacount(SeqAA, 'Others', 'full', 'Structure', 'full') — Displays fields for 20 amino acids, 3 ambiguous amino acids, stops, gaps, and an Others field. If there are unknown characters, add the counts to the Others field; otherwise displays 0 in the Others field.

Examples

Create an amino acid sequence.
```
Seq = 'MATLAB';
```

Count the amino acids in the sequence and return the results in a structure.

AA =  aacount(Seq)

Warning: Ambiguous symbols 'B' appear in the sequence. These will be in Others.

AA = 

     A: 2
     R: 0
     N: 0
     D: 0
     C: 0
     Q: 0
     E: 0
     G: 0
     H: 0
     I: 0
     L: 1
     K: 0
     M: 1
     F: 0
     P: 0
     S: 0
     T: 1
     W: 0
     Y: 0
     V: 0
Others: 1

Get the count for alanine (A) residues.
```
AA.A

ans =

       2
```

Create a random character string to represent an amino acid sequence.

Seq = randseq(20, 'alphabet', 'amino')

Seq =

   dwcztecakfuecvifchds

Count the amino acids in the sequence, return the results in a structure, and display the results in a pie chart.
```
AA =  aacount(Seq, 'chart', 'pie');
```