doc/speed_comparison.md

In richelbilderbeek/pureseqtmr: Predict Transmembrane Protein Topology

pureseqtmr speed comparison

pureseqtmr versus tmhmm

tmhmm predict membrane protein topology at three levels (inside, outside, membrane), one does need to fill in a registration form, as it is for academic users only.

This scripts demonstrates that PureseqTM is approximately 100x slower than TMHMM:

fasta_filename <- system.file("extdata", "UP000464024.fasta", package = "pureseqtmr")
system.time({tmhmm::predict_topology(fasta_filename = fasta_filename)})
system.time({pureseqtmr::predict_topology(fasta_filename = fasta_filename)})

Results:

> system.time({tmhmm::predict_topology(fasta_filename = fasta_filename)})
   user  system elapsed 
  1.723   0.008   1.733 
> system.time({pureseqtmr::predict_topology(fasta_filename = fasta_filename)})
   user  system elapsed 
117.511   1.746  85.748 

Also when running these tools from scripts, the results are similar:

time ./bin/decodeanhmm.Linux_x86_64 lib/TMHMM2.0.model UP000464024.fasta -f lib/TMHMM2.0.options
[...]
real    0m1.379s
user    0m1.375s
sys 0m0.004s

time ./PureseqTM_proteome.sh -i UP000464024.fasta 
71
real    0m53.471s
user    1m36.354s
sys 0m1.426s

richelbilderbeek/pureseqtmr documentation built on April 16, 2023, 1:19 p.m.