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