proteinalign

Documentation

'proteinalign' is a R package that performs protein alignment using statistical shape analysis techiniques.

Installation

'proteinalign' depends on the Bioconductor's packages of 'Biostrings' and 'msa' which can be installed using

source('https://bioconductor.org/biocLite.R')
biocLite('Biostrings')
biocLite('msa')

Next, 'proteinalign' can be installed from the github repository using

install.packages('devtools')
devtools::install_github('thodorisgkolias/proteinalign')

and it can be loaded in R as usually with

library(proteinalign)

Code example

Load data

data1 <- LoadPDB('2gb1')
data2 <- LoadPDB('1ubq')

then putting it in a list using

data <- list(data1,data2)

Finally you can produce an alignment of these two protein molecules using

ProteinAlign(data, SP = 7, n.cores = 8)

Authors

License

GPL (>=2)