Includes functions 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.
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
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:
If you have devtools installed, install the latest stable version this package directly from GitHub:
library(devtools) install_github("dosorio/Peptides") library(Peptides)
|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|
|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|
|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|
|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)|
Osorio, D., Rondon-Villarreal, P. & Torres, R. Peptides: A package for data mining of antimicrobial peptides. The R Journal. 7(1), 4–14 (2015).
D. Osorio, P. Rondón-Villarreal and R. Torres. Peptides: Calculate indices and theoretical physicochemical properties of peptides and protein sequences., 2014. URL: http: //CRAN.R-project.org/package=Peptides. R Package Version 2.2.
The charge and pI functions were rewritten in C++ and an optimization approach was used thanks to Scott McCain (@jspmccain) and Timothée Poisot (@tpoisot) suggestion.
An error in zScales function data was solved. Q and E values were wrongly interchanged in v 2.0.
All datasets were unified into AAdata
All test were migrated to testthat
readXVG and plotXVG functions were improved by J. Sebastian Paez
kideraFactors output vector was renamed as KF#
Now all sequences are checked before to property calculation
aaDescriptos, fasgaiVectors, blosumIndices, mswhimScores, zScales, vhseScales, protFP, tScales and stScales functions were added
Four new functions were added: autoCorrelation, autoCovariance, crossCovariance and crucianiProperties
Functions related with XVG files were updated.
Documentation was changed to roxygen2
All functions were re-vectorized to support set of peptides as input
Kidera function now returns all factors in a unique output
The mw function now computes the molecular weight using monoisotopic values
A problem with blank spaces was solved
A instaindex function bug has been fixed.
A problem with line breaks in sequences was solved.
A membpos function bug has been fixed.
The results now are not rounded.
Hydrophobicity function now can compute the GRAVY index with one of the 38 scales includes in Peptides (*new):
The mw function has been fixed to give the same result as ExPASy pI/mw tool.
The hmoment function is now vectorized and allow adjust the windows size. (thanks to an anonymous reviewer of RJournal).
The pepdata dataset and the variable name are now unified to lowercases.
The seqinr package dependency was removed.