Functions for obtaining N-sp predictions based on protein sequence.
get_signalp5()
Query SignalP 5.0 web server.
get_signalp()
Query SignalP web server.
get_targetp()
Query TargetP web server.
get_phobius()
Query Phobius web server.
Functions for obtaining GPI predictions based on protein sequence.
get_big_pi()
Query big-PI Plant Predictor web server.
get_pred_gpi()
Query PredGPI web server.
get_netGPI()
Query NetGPI - 1.1 web server.
Functions for domain, transmembrane region and disorder prediction based on protein sequence.
get_hmm()
Query hmmer web server.
get_cdd()
Query the Conserved Domain Database.
get_espritz()
Query Espritz web server.
pfam2go()
Add GO terms based on pfam accessions
get_tmhmm()
Query TMHMM-2.0 web server.
predict_hyp()
Predict hydroxyproline positions in plant proteins based on primary structure
scan_ag()
Find AG glycomodules in protein sequences
maab()
MAAB classification of hydroxyproline rich glycoproteins
plot_prot()
Protein structure diagram.
scan_nglc()
Detection of motifs for N-glycosylation on asparagine residues.
Data frame with 2700 Arabidopsis thaliana protein sequences predicted to contain a N-sp by either Phobius or SignalP with length of 100 - 400 amino acids.
at_nsp
2700 Arabidopsis thaliana protein sequences.
CTDC()
Composition descriptor (CTDC)
getAAindex()
Extract amino acid attributes
getKmer()
Extract simetric k-mers around prolines
extractMBdesc()
Normalized Moreau-Broto Autocorrelation Descriptor
QSOlevel()
Quasi-Sequence-Order (QSO) Descriptor
sub_hyp()
Substitute prolines to hydroxyprolines
split_fasta()
Split a fasta formatted file.