Bioinformatics Toolbox

aacount

Count the amino acids in a sequence

Syntax

Amino = aacount(SeqAA, 'PropertyName', PropertyValue...) aacount(...,'Chart', ChartValue) aacount(...,'Others', OthersValue) aacount(..., 'Structure', StructureValue)

Arguments

`SeqAA`	Amino acid sequence. Enter a character string or vector of integers from the table . Examples: `'ARN'` or `[1 2 3]`. You can also enter a structure with the field `Sequence`.
`Chart`	Property to select a type of plot. Enter either `'pie'` or `'bar'.`
`Others`	Property to control the counting of ambiguous characters individually. Enter either `'full'` or `'bundle'`. The default value is `'bundle'`.

Description

Amino = aacount(SeqAA, 'PropertyName', PropertyValue...) counts the type and number of amino acids in an amino acid sequence (SeqAA) and returns the counts in a 1-by-1 structure (Amino) with 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 V ).

If a sequence contains amino acids with ambiguous characters (B, Z, X), the stop character (*), or gaps indicated with a hyphen (-), the field Others is added to the structure and a warning message is displayed.
```
Warning: Symbols other than the standard 20 amino acids
appear in the sequence
```

If a sequence contains any characters other than the 20 standard amino acids, ambiguous characters, stop, and gap characters, the characters are counted in the field Others and a warning message is displayed.
```
Warning: Sequence contains unknown characters. These will
be ignored.
```

If the property Others = 'full' , this function lists the ambiguous characters separately, asterisks are counted in a new field (Stop), and hyphens are counted in a new field, (Gap).

aacount(...,'Chart', ChartValue) creates a chart showing the relative proportions of the amino acids.

aacount(...,'Others', OthersValue), when OthersValue is 'full'', counts the ambiguous amino acid characters individually instead of adding them together in the field Others.

aacount(..., 'Structure', StructureValue) when StructureValue is 'full', blocks the unknown characters warning and ignores counting unknown characters.

aacount(SeqAA) — Display 20 amino acids, and only if there are ambiguous and unknown characters, add an Others field with the counts.
aacount(SeqAA, 'Others', 'full') — Display 20 amino acids, 3 ambiguous amino acids, stops, gaps, and only if there are unknown characters, add an Others field with the unknown counts.
aacount(SeqAA, 'Structure', 'full') — Display 20 amino acids and always display an Others field. If there are ambiguous and unknown characters, adds counts to the Others field otherwise display 0.
aacount(SeqAA, 'Others', 'full', 'Structure', 'full') — Display 20 amino acids, 3 ambiguous amino acids, stops, gaps, and Others field. If there are unknown characters, add counts to the Others field otherwise display 0.

Examples

Count the amino acids in the string 'MATLAB'.

AA  = aacount('MATLAB')

Warning: Symbols other than the standard 20 amino acids appear
in the sequence.
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

AA.A
ans =
       2

aacount

Syntax

Arguments

Description

Examples

See Also