predict_topology_from_sequence: Run PureseqTM directy on a protein sequence

In pureseqtmr: Predict Transmembrane Protein Topology

Run PureseqTM directy on a protein sequence

Description

Will stop if the protein sequence is shorter than three amino acids.

Usage

predict_topology_from_sequence(
  protein_sequence,
  folder_name = get_default_pureseqtm_folder(),
  temp_fasta_filename = tempfile(fileext = ".fasta")
)

Arguments

protein_sequence	a protein sequence, with the amino acids as capitals, for example MEILCEDNTSLSSIPNSL
folder_name	superfolder of PureseqTM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_pureseqtm_folder
temp_fasta_filename	temporary FASTA filename, which will deleted after usage

Value

a topology as a string of zeroes and ones, where a one denotes that the corresponding amino acid is located within the membrane.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  protein_sequence <- paste0(
    "QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLM",
    "SLAIADMLLGFLVMPVSMLTILYGYRWP"
  )
  predict_topology_from_sequence(protein_sequence)
}

pureseqtmr documentation built on April 6, 2023, 5:20 p.m.