Awesome

`pureseqtmr`

Branch
`master`
`develop`

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)

SARS-CoV-2 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

References

Article about PureseqTM:

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