knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
This demo shows how to estimate the location of the amino acids in a
membrane protein. This package tmhmm
uses the tool TMHMM to do so.
The amino acids of a membrane protein are estimated to be either
inside the cell (the cytosol side), outside of the cell (the surroundings
of the cell) or in the transmembrane part.
Load the library:
library(tmhmm)
For this vignette to work, TMHMM must have been installed.
TMHMM can be installed using install_tmhmm
, but this does
require a download link that must be requested from
https://services.healthtech.dtu.dk/service.php?TMHMM-2.0.
install_tmhmm("https://services.healthtech.dtu.dk/download/28c408dc-ef5e-47ad-a284-66754bcd27f7")
The TMHMM installation is checked here, with the goal of producing a helpful error message:
check_tmhmm_installation()
We need a FASTA file to work on:
fasta_filename <- system.file("extdata", "tmhmm.fasta", package = "tmhmm") cat(readLines(fasta_filename), sep = "\n")
Estimating the locations of the amino acids:
if (is_tmhmm_installed()) { locatome <- run_tmhmm(fasta_filename) cat(locatome, sep = "\n") }
The legend of these locations:
Character|Location
---------|---------------------
i
|Inside or cytosol-side
o
|Outside or surroundings-side
M
|Transmembrane
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