richelbilderbeek / pureseqtmr

R package to work with PureseqTM

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 PureseqTM

Due to CRAN policy, pureseqtmr cannot install PureseqTM. As a workaround, the non-CRAN pureseqtmrinstall can be used.

To install PureseqTM:

remotes::install_github("richelbilderbeek/pureseqtmrinstall")
pureseqtmrinstall::install_pureseqtm()

How to convert a FASTA file to a PureseqTM topolgy file?

Combine predict_topology and save_tibble_as_fasta_file:

library(pureseqtmr)

save_tibble_as_fasta_file(
  predict_topology(fasta_filename = "my.fasta"),
  fasta_filename = "my.topo"
)

Are there similar packages?

These are the ones I use:

• tmhmm: predict membrane protein topology at three levels (inside, outside, membrane),
  do need registration form, as it is for academic users only. See here for a run-time speed comparison. Spoiler: PureseqTM is approximately 20x slower than TMHMM

What happens to a selenocystein (U) in the sequence?

pureseqtmr gives an error.

PureseqTM ignores the selenocystein, as it does with any character.

What happens to short sequences?

pureseqtmr package gives an error.

PureseqTM prints out a message and returns a zero-length topology.

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.