README.md

In dosorio/Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

Peptides ======== R package to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package

Install

This package required R version 1.2.2 or higher. If you are using an older version of R you will be prompted to upgrade when you try to install the package.

The official release of Peptides is available on CRAN. To install from CRAN, use the following command:

install.packages("Peptides", dependencies=TRUE)

If you have devtools installed, install the latest stable version this package directly from GitHub:

library(devtools)
install_github("dosorio/Peptides")
library(Peptides)

Available functions

| Code | Function | | :------------- |:-------------| |aaList| Return a vector with the 20 standard aminoacids in upper case| |aaComp | Compute the amino-acid composition of a protein sequence| |aaDescriptors|Compute 66 descriptors for each amino acid of a protein sequence| |aIndex | Compute the aliphatic index of a protein sequence | |autoCorrelation|Compute the auto-correlation index of a protein sequence| |autoCovariance|Compute the auto-covariance index of a protein sequence| |blosumIndices|Compute the BLOSUM62 derived indices of a protein sequence| |boman | Compute the Boman (Potential Protein Interaction) index | |charge | Compute the theoretical net charge of a protein sequence | |crossCovariance|Compute the cross-covariance index of a protein sequence| |crucianiProperties | Compute the Cruciani properties of a protein sequence | |fasgaiVectors| Compute the FASGAI vectors of a protein sequence | |hmoment | Compute the hydrophobic moment of a protein sequence | |hydrophobicity | Compute the hydrophobicity index of a protein sequence | |instaIndex | Compute the instability index of a protein sequence | |kideraFactors | Compute the Kidera factors of a protein sequence | |lengthpep| Compute the aminoacid length of a protein sequence | |massShift | Compute the mass difference of a protein sequence labelled with stable isotope. | |membpos | Compute theoretically the class of a protein sequence | |mswhimScores|Compute the MS-WHIM scores of a protein sequence| |mw | Compute the molecular weight of a protein sequence | |mz | Compute the mass over charge (m/z) of a protein sequence | |pI | Compute the isoelectic point (pI) of a protein sequence | |plotXVG | Plot time series from GROMACS XVG files | |protFP|Compute the protFP descriptors of a protein sequence| |readXVG | Read XVG files from GROMACS molecular dynamics package | |stScales| Compute the ST-scales of a protein sequence| |tScales| Compute the T-scales of a protein sequence| |vhseScales|Compute the VHSE-scales of a protein sequence| |zScales| Compute the Z-scales of a protein sequence |

Available datasets

| Code | Description | |:----------- |:------------| |AAdata | Properties, scales and indices for the 20 naturally occurring amino acids from various sources | |pepdata | A data frame with 21 physicochemical properties and indices from 100 amino-acid sequences (50 antimicrobial and 50 non antimicrobial) |

Citation

Osorio, D., Rondon-Villarreal, P. & Torres, R. Peptides: A package for data mining of antimicrobial peptides. The R Journal. 7(1), 4–14 (2015).

dosorio/Peptides documentation built on Jan. 4, 2024, 2:28 p.m.