aacount - Count amino acids in sequence

Syntax

Input 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]
AmbiguousValue	String specifying how to treat ambiguous amino acid characters (B, Z, or X). Choices are: 'ignore' (default) — Skips ambiguous characters 'bundle' — Counts ambiguous characters and reports the total count in the Ambiguous field. 'prorate' — Counts ambiguous characters and distributes them proportionately in the appropriate fields. For example, the counts for the character B are distributed evenly between the D and N fields. 'individual' — Counts ambiguous characters and reports them in individual fields. 'warn' — Skips ambiguous characters symbols and displays a warning.
GapsValue	Specifies whether gaps, indicated by a hyphen (-), are counted or ignored. Choices are true or false (default).
ChartValue	String specifying a chart type. Choices are 'pie' or 'bar'.

Output Arguments

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).

• Ambiguous amino acid characters (B, Z, or X), gaps, indicated by a hyphen (-), and end terminators (*) are ignored by default.

• Unrecognized characters are ignored and cause the following warning message.

  Warning: Unknown symbols appear in the sequence. These will be ignored.

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, ...'Ambiguous', AmbiguousValue, ...) specifies how to treat ambiguous amino acid characters (B, Z, or X). Choices are:

• 'ignore' (default)

• 'bundle'

• 'prorate'

• 'individual'

• 'warn'

AAStruct = aacount(SeqAA, ...'Gaps', GapsValue, ...) specifies whether gaps, indicated by a hyphen (-), are counted or ignored. Choices are true or false (default).

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

Examples

1. Create an amino acid sequence.

   Seq = 'MATLAB';

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

   AA =  aacount(Seq)
   
   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
   

3. Get the count for alanine (A) residues.

   AA.A
   
   ans =
   
          2

4. Use the fastaread function to read the sequence for the human p53 tumor protein into a MATLAB structure.

   p53 = fastaread('p53aa.txt')
   
   p53 = 
   
         Header: 'gi|8400738|ref|NP_000537.2| tumor protein p53 [Homo sapiens]'
       Sequence: [1x393 char]

5. Count the amino acids in the sequence, return the results in a structure, and display the results in a pie chart.

   AA =  aacount(p53, 'chart', 'pie');

   

See Also

aminolookup | atomiccomp | basecount | codoncount | dimercount | isoelectric | molweight | proteinplot | proteinpropplot | seqtool

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