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).