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