run_tmhmm_on_sequence: Run TMHMM directy on a protein sequence

In richelbilderbeek/tmhmm: Interface to TMHMM

Run TMHMM directy on a protein sequence

Description

Run TMHMM directy on one protein sequence

Usage

run_tmhmm_on_sequence(
  protein_sequence,
  folder_name = get_default_tmhmm_folder()
)

Arguments

protein_sequence	a protein sequence, with the amino acids as capitals, for example 'MEILCEDNTSLSSIPNSL'
folder_name	superfolder of TMHMM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_tmhmm_folder

Value

the topology. The topology is a character string with the same length as the protein sequence. The topology consists of the characters i ('inside'), I ('inside'), m ('membrane'), M ('membrane'), o ('outside') and O ('outside')

Examples

if (is_tmhmm_installed()) {
  protein_sequence <- paste0(
    "QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLM",
    "SLAIADMLLGFLVMPVSMLTILYGYRWP"
  )
  run_tmhmm_on_sequence(protein_sequence)
}

richelbilderbeek/tmhmm documentation built on Sept. 3, 2022, 5:14 p.m.