Phobius web server is a combined transmembrane topology and signal peptide (N-sp) predictor. Currently only "normal prediction" of signal peptides is supported by the function.
get_phobius(data, ...) # S3 method for character get_phobius(data, progress = FALSE, ...) # S3 method for data.frame get_phobius(data, sequence, id, ...) # S3 method for list get_phobius(data, ...) # S3 method for default get_phobius(data = NULL, sequence, id, ...) # S3 method for AAStringSet get_phobius(data, ...)
| data | A data frame with protein amino acid sequences as strings in one column and corresponding id's in another. Alternatively a path to a .fasta file with protein sequences. Alternatively a list with elements of class |
|---|---|
| ... | currently no additional arguments are accepted apart the ones documented bellow. |
| progress | Boolean, whether to show the progress bar, at default set to FALSE. |
| sequence | A vector of strings representing protein amino acid sequences, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank. |
| id | A vector of strings representing protein identifiers, or the appropriate column name if a data.frame is supplied to data argument. If .fasta file path, or list with elements of class "SeqFastaAA" provided to data, this should be left blank. |
A data frame with columns:
Character, name of the submitted sequence.
Integer, the number of predicted transmembrane segments.
Character, Y/0 indicator if a signal peptide was predicted or not.
Character string, predicted topology of the protein.
Integer, first amino acid after removal of the signal peptide
Logical, did Phobius predict the presence of a signal peptide
Integer, length of the predicted signal peptide.
The topology (prediction column of the result) is given as the position of the transmembrane helices separated by 'i' if the loop is on the cytoplasmic or 'o' if it is on the non-cytoplasmic side. A signal peptide is given by the position of its h-region separated by a n and a c, and the position of the last amino acid in the signal peptide and the first of the mature protein separated by a /.
This function creates temporary files in the working directory.
Kall O. Krogh A. Sonnhammer E. L. L. (2004) A Combined Transmembrane Topology and Signal Peptide Prediction Method. Journal of Molecular Biology 338(5): 1027-1036
library(ragp) data(at_nsp) phobius_pred <- get_phobius(at_nsp[1:20,], sequence, Transcript.id) phobius_pred#> id tm sp prediction cut_site is.phobius #> 1 ATCG00660.1 0 Y n17-24c29/30o 30 TRUE #> 2 AT2G43600.1 0 Y n6-17c22/23o 23 TRUE #> 3 AT2G28410.1 0 Y n6-17c22/23o 23 TRUE #> 4 AT2G22960.1 0 Y n8-16c20/21o 21 TRUE #> 5 AT2G19580.1 3 Y n7-18c26/27o42-64i71-95o233-253i 27 TRUE #> 6 AT2G19690.2 0 Y n10-23c28/29o 29 TRUE #> 7 AT2G19690.1 0 Y n10-23c28/29o 29 TRUE #> 8 AT2G33130.1 0 Y n7-20c26/27o 27 TRUE #> 9 AT2G05520.1 0 Y n5-18c23/24o 24 TRUE #> 10 AT2G05520.2 0 Y n5-18c23/24o 24 TRUE #> 11 AT2G05520.3 0 Y n5-18c23/24o 24 TRUE #> 12 AT2G05520.4 0 Y n5-18c23/24o 24 TRUE #> 13 AT2G05520.6 0 Y n5-18c23/24o 24 TRUE #> 14 AT2G05520.5 0 Y n5-18c23/24o 24 TRUE #> 15 AT2G04031.1 0 Y n8-16c24/25o 25 TRUE #> 16 AT2G43620.1 0 Y n11-21c28/29o 29 TRUE #> 17 AT2G37390.1 0 Y n6-16c24/25o 25 TRUE #> 18 AT2G37390.2 0 Y n6-16c24/25o 25 TRUE #> 19 AT2G35250.1 0 Y n5-16c21/22o 22 TRUE #> 20 AT2G38390.1 0 Y n7-22c29/30o 30 TRUE #> sp.length #> 1 29 #> 2 22 #> 3 22 #> 4 20 #> 5 26 #> 6 28 #> 7 28 #> 8 26 #> 9 23 #> 10 23 #> 11 23 #> 12 23 #> 13 23 #> 14 23 #> 15 24 #> 16 28 #> 17 24 #> 18 24 #> 19 21 #> 20 29