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R package for TMHMM [1, 2], to predict transmembrane helices in proteins.
Please note that this page is intended for academic users only. Other users are requested to contact the Software Package Manager at [email protected]
usethis::install_github("richelbilderbeek/tmhmm")
Install TMHMM to a default folder:
library(tmhmm)
install_tmhmm("http://www.cbs.dtu.dk/download/D3198788-0F1D-11E9-883C-84B3B9CD16B5/")
The URL can be obtained by requesting a download link at
the TMHMM website
at https://services.healthtech.dtu.dk/service.php?TMHMM-2.0.
As this URL expires after four hours, tmhmm cannot do this for you.
We need a FASTA file to work on:
fasta_filename <- system.file("extdata", "tmhmm.fasta", package = "tmhmm")
The FASTA file should contain the protein sequences of one or more genes. Reading the file ...
cat(readLines(fasta_filename), sep = "\n")
results in:
>5H2A_CRIGR you can have comments after the ID
MEILCEDNTSLSSIPNSLMQVDGDSGLYRNDFNSRDANSSDASNWTIDGENRTNLSFEGYLPPTCLSILHL
QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYRWP
LPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGVSMPIPVF
GLQDDSKVFKQGSCLLADDNFVLIGSFVAFFIPLTIMVITYFLTIKSLQKEATLCVSDLSTRAKLASFSFL
PQSSLSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNE
HVIGALLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENRKPLQLILVNTIPALAYKSSQLQA
GQNKDSKEDAEPTDNDCSMVTLGKQQSEETCTDNINTVNEKVSCV
Use run_tmhmm to estimate the location of the amino acids
using TMHMM:
locatome <- run_tmhmm(fasta_filename)
TMHMM will return a 'locatome': the location of each amino acid:
i: insideo: outsideM: membrane
Here is how it looks like:
cat(locatome, sep = "\n")
>5H2A_CRIGR you can have comments after the ID
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooMMMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMoooooooooo
ooooMMMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMoo
oooooooooooooooooMMMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMMMoooooooooMMMM
MMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
tmhmm can only work on the set of operating systems TMHMM
works on. Currently, only Linux is supported:
| Operating system | Supported by TMHMM | Supported by tmhmm |
|---|---|---|
| AIX | Y | N |
| IRIX32 | Y | N |
| IRIX64 | Y | N |
| Linux | Y | Y |
| MacOS | N | N |
| OSF1 | Y | N |
| SunOS | Y | N |
| Windows | N | N |
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[1] A. Krogh, B. Larsson, G. von Heijne, and E. L. L. Sonnhammer. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. Journal of Molecular Biology, 305(3):567-580, January 2001.
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[2] E. L.L. Sonnhammer, G. von Heijne, and A. Krogh. A hidden Markov model for predicting transmembrane helices in protein sequences. In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 175-182, Menlo Park, CA, 1998. AAAI Press.