R: Compute the amino acid composition of a protein sequence

aaComp {Peptides} | R Documentation

## Compute the amino acid composition of a protein sequence

### Description

This function calculates the amount of amino acids of a particular class and classified as: Tiny, Small, Aliphatic, Aromatic, Non-polar, Polar, Charged, Basic and Acidic based on their size and R-groups using same function implemented in EMBOSS 'pepstat'. The output is a matrix with the number and percentage of amino acids of a particular class

### Usage

    aaComp(seq)

### Arguments

`seq` | An amino-acid sequence

### Details

Amino acids are zwitterionic molecules with an amine and a carboxyl group present in their structure. Some amino acids possess side chains with specific properties that allow grouping them in different ways. The `aaComp` function classifies amino acids based on their size, side chains, hydrophobicity, charge and their response to pH 7.

### Value

The output is a matrix with the number and percentage of amino acids of a particular class

- Tiny (A + C + G + S + T)

- Small (A + B + C + D + G + N + P + S + T + V)

- Aliphatic (A + I + L + V)

- Aromatic (F + H + W + Y)

- Non-polar (A + C + F + G + I + L + M + P + V + W + Y)

- Polar (D + E + H + K + N + Q + R + S + T + Z)

- Charged (B + D + E + H + K + R + Z)

- Basic (H + K + R)

- Acidic (B + D + E + Z)

### Note

This function was originally written by Alan Bleasby (ajb@ebi.ac.uk) for the EMBOSS package. Further information: http://emboss.sourceforge.net/apps/cvs/emboss/apps/pepstats.html

### References

Rice, Peter, Ian Longden, and Alan Bleasby. "EMBOSS: the European molecular biology open software suite." Trends in genetics 16.6 (2000): 276-277.

### Examples

    # COMPARED TO PEPSTATS
    # http://emboss.bioinformatics.nl/cgi-bin/emboss/pepstats
    # Property      Residues              Number  Mole%
    # Tiny          (A+C+G+S+T)             4   19.048
    # Small         (A+B+C+D+G+N+P+S+T+V)   4   19.048
    # Aliphatic     (A+I+L+V)               5   23.810
    # Aromatic      (F+H+W+Y)               5   23.810
    # Non-polar     (A+C+F+G+I+L+M+P+V+W+Y) 11  52.381
    # Polar         (D+E+H+K+N+Q+R+S+T+Z)   9   42.857
    # Charged       (B+D+E+H+K+R+Z)         8   38.095
    # Basic         (H+K+R)                 8   38.095
    # Acidic        (B+D+E+Z)               0   00.000

    ## AA composition of PDB: 1D9J Cecropin Peptide
    aaComp(seq= "KWKLFKKIGIGKFLHSAKKFX")

    ## Output
    #           Number  Mole %
    # Tiny           4 19.048
    # Small          4 19.048
    # Aliphatic      5 23.810
    # Aromatic       5 23.810
    # NonPolar      11 52.381
    # Polar          9 42.857
    # Charged        8 38.095
    # Basic          8 38.095
    # Acidic         0  0.000

[Package Peptides version 2.4.4 Index]