run_signalHsmm: Predict presence of signal peptide in protein

In signalHsmm: Predict Presence of Signal Peptides

Description

Using the hidden semi-Markov model predict presence of signal peptide in eukaryotic proteins.

Usage

run_signalHsmm(test_data)

Arguments

test_data

single protein sequence (character vector) or list of sequences. It may be an object of class SeqFastaAA.

Details

Function signalHsmm returns respectively probability of presence of signal peptide, start of signal peptide and the probable cleavage site localization. If input consists of more than one sequence, result is a data.frame where each column contains above values for different proteins.

Value

An object of class hsmm_pred_list.

Note

Currently start of signal peptide is naively set as 1 amino acid. The prediction of a cleavage site is still an experimental feature, use on your own risk.

See Also

hsmm_pred_list hsmm_pred

Examples

#run signalHsmm on one sequence
x1 <- run_signalHsmm(benchmark_dat[[1]])

#run signalHsmm on one sequence, but input is a character vector
x2 <- run_signalHsmm(c("M", "A", "G", "K", "E", "V", "I", "F", "I", "M", "A", "L", 
"F", "I", "A", "V", "E", "S", "S", "P", "I", "F", "S", "F", "D", 
"D", "L", "V", "C", "P", "S", "V", "T", "S", "L", "R", "V", "N", 
"V", "E", "K", "N", "E", "C", "S", "T", "K", "K", "D", "C", "G", 
"R", "N", "L", "C", "C", "E", "N", "Q", "N", "K", "I", "N", "V", 
"C", "V", "G", "G", "I", "M", "P", "L", "P", "K", "P", "N", "L", 
"D", "V", "N", "N", "I", "G", "G", "A", "V", "S", "E", "S", "V", 
"K", "Q", "K", "R", "E", "T", "A", "E", "S", "L"))

#run signalHsmm on list of sequences
x3 <- run_signalHsmm(benchmark_dat[1:3])
#see summary of results
summary(x3)
#print results as data frame
pred2df(x3)
#summary one result
summary(x3[[1]])
plot(x3[[1]])

Example output

Number of proteins tested: 3
Number of proteins with signal peptide: 3
            sp.probability is.signal sp.start sp.end
33VP_CHENC       0.9622174      TRUE        1     21
3L21_AUSLA       0.8969475      TRUE        1     21
3NO22_MICCO      0.8206804      TRUE        1     23

Probability of signal peptide presence: 0.9622
Signal peptide detected.

The prediction of the regional structure is an experimental feature, use at your own risk.
Start of signal peptide: 1
End of signal peptide: 21
n-region (length 5):
         MAGKE

h-region (length 11):
         VIFIMALFIAV

c-region (length 4):
         ESSP

signalHsmm documentation built on May 1, 2019, 7:55 p.m.