pureseqtmr

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R package to work with PureseqTM.

Because PureseqTM only works on Linux, pureseqtmr only works on Linux.

Example

library(pureseqtmr)

# Use an example proteome
fasta_filename <- system.file(
  "extdata", 
  "UP000464024.fasta", 
  package = "pureseqtmr"
)

# Predict the topology
topology <- predict_topology(fasta_filename)

# Simplify the protein names
topology$name <- stringr::str_match(
  string = topology$name,
  pattern = "..\\|.*\\|(.*)_SARS2"
)[,2]

# Plot the topology
plot_topology(topology)

Install

Install the package:

remotes::install_github("richelbilderbeek/pureseqtmr")

Install PureseqTM to a default folder:

pureseqtmr::install_pureseqtm()

There is a feature I miss

See CONTRIBUTING, at Submitting use cases

I want to collaborate

See CONTRIBUTING, at 'Submitting code'

I think I have found a bug

See CONTRIBUTING, at 'Submitting bugs'

There's something else I want to say

Sure, just add an Issue. Or send an email.

External links

• PureseqTM GitHub repo
• PureseqTM server

References

Article about PureseqTM:

• Wang, Qing, et al. "Efficient and accurate prediction of transmembrane topology from amino acid sequence only." bioRxiv (2019): 627307.