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signalHsmm (version 1.3)

Predict Presence of Signal Peptides

Description

Predicts presence of signal peptides in eukaryotic protein using hidden semi-Markov models. The implemented algorithm can be accessed both from command line and GUI.

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Install

install.packages('signalHsmm')

Monthly Downloads

205

Version

1.3

License

GPL-3

Issues

1

Pull Requests

0

Stars

2

Forks

0

Maintainer

Michal Burdukiewicz

Last Published

July 3rd, 2015

Functions in signalHsmm (1.3)

benchmark_dat

Benchmark data set for signalHsmm
train_hsmm

Train sighsmm_model object
pred2df

Convert list of signalHsmm predictions
gui_signalHsmm

GUI for signalHsmm
summary.hsmm_pred_list

Summarize list of signalHsmm predictions
plot.hsmm_pred

Plot single signalHsmm prediction
summary.hsmm_pred

Summarize single signalHsmm prediction
predict.sighsmm_model

Predict sighsmm_model object
run_signalHsmm

Predict presence of signal peptide in protein
signalHsmm

signalHsmm - prediction of signal peptides
hsmm_pred_list

hsmm_pred_list class
read_txt

Read sequences from .txt file
find_nhc

Localize n-, h- and c-region in signal peptide
duration_viterbi

Compute most probable path with extended Viterbi algorithm.
is_protein

Protein test
aaaggregation

Scheme for amino acid aggregation
hsmm_pred

hsmm_pred class
add_k_mer_state

Adds k-mer hidden state to signalHsmm model
read_uniprot

Read data from UniProt database