tmhmm: predict transmembrane domains with TMHMM
In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description Usage Arguments Value Examples

This function calls local TMHMM to predict transmembarne domains in protein sequence.

In the full-length proteins N-terminal signal peptide could be erroneously predicted as a TM domain. Therefore it is recommended to run TMHMM on mature pepetide sequences (with clipped signal peptides) to avoid false positive predictions.

To generate an CBSResult object with mature sequences please run signalp predictions first.

1	tmhmm(input_obj, TM, paths = NULL)

`input_obj`	an instance of SignalpResult class, input should contain mature_fasta slot;
`TM`	allowed number of TM domains in mature peptides, recommended value <= 1; use TM = 0 for strict filtering
`paths`	if tmhmm is not acessible globally, a file conatining a full path to it's executable should be provided; for details please check SecretSanta vignette.

TMhmmResult object

aa <- readAAStringSet(system.file("extdata", "sample_prot_100.fasta",
package = "SecretSanta"))
inp <- CBSResult(in_fasta = aa[1:20])
s1_sp2 <- signalp(inp, version = 2, organism = 'euk', run_mode = "starter",
legacy_method = 'hmm')
tm <- tmhmm(s1_sp2, TM = 1)