add_physicochemical_properties_to_HMMER_tbl: Add EMBOSS-inspired theoretical physicochemical properties...

In currocam/utilsHMMER: HMMERutils

Add EMBOSS-inspired theoretical physicochemical properties using the Peptides library to an AnnotatedDataFrame

Description

Add EMBOSS-inspired theoretical physicochemical properties using the Peptides library to an AnnotatedDataFrame

Usage

add_physicochemical_properties_to_HMMER_tbl(data, colname = "hits.fullfasta")

Arguments

data	A Data Frame containig the indicated column with protein sequences.
colname	A single character vector with the name of the column with the protein sequences. This documentation is based on the following documentation: https://github.com/dosorio/Peptides/

Value

A Data Frame with new columns with the theoretical physicochemical properties

Theoretical properties

• molecular.weight: sum of the masses of each atom constituting a molecule (Da) using the same formulas and weights as ExPASy's.

• charge: net charge of a protein sequence based on the Henderson-Hasselbalch equation using Lehninger pKa scale.

• pI: isoelectric point calculated as in EMBOSS PEPSTATS.

• mz: mass over charge ratio (m/z) for peptides, as measured in mass spectrometry.

• aIndex: aliphatic index of a protein. The aindex is defined as the relative volume occupied by aliphatic side chains (Alanine, Valine, Isoleucine, and Leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins.

• boman: potential protein interaction index . The index is equal to the sum of the solubility values for all residues in a sequence, it might give an overall estimate of the potential of a peptide to bind to membranes or other proteins as receptors, to normalize it is divided by the number of residues. A protein have high binding potential if the index value is higher than 2.48.

• hydrophobicity: GRAVY hydrophobicity index of an amino acids sequence using KyteDoolittle hydophobicity scale.

• instaIndex: Guruprasad's instability index. This index predicts the stability of a protein based on its amino acid composition, a protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable.

• STYNQW: Percentage of amino acids (S + T + Y + N + Q + W)

• Tiny: Percentage of amino acids (A + C + G + S + T)

• Small: Percentage of amino acids (A + B + C + D + G + N + P + S + T + V)

• Aliphatic: Percentage of amino acids (A + I + L + V)

• Aromatic: Percentage of amino acids (F + H + W + Y)

• Nonpolar': Percentage of amino acids (A + C + F + G + I + L + M + P + V + W + Y)

• Polar: Percentage of amino acids (D + E + H + K + N + Q + R + S + T + Z)

• Charged: Percentage of amino acids (B + D + E + H + K + R + Z)

• Basic: Percentage of amino acids (H + K + R)

• Acidic: Percentage of amino acids (B + D + E + Z)

Examples

data(phmmer_2abl)
add_physicochemical_properties_to_HMMER_tbl(
    data = phmmer_2abl,
    colname = "hits.fullfasta"
)

currocam/utilsHMMER documentation built on Feb. 19, 2023, 9:54 p.m.