get_phobius: Query Phobius web server.

In missuse/ragp: Mining for Hydroxyproline rich glycoprotein sequences

Description

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.

Usage

get_phobius(data, ...)

## S3 method for class 'character'
get_phobius(data, progress = FALSE, ...)

## S3 method for class 'data.frame'
get_phobius(data, sequence, id, ...)

## S3 method for class 'list'
get_phobius(data, ...)

## Default S3 method:
get_phobius(data = NULL, sequence, id, ...)

## S3 method for class 'AAStringSet'
get_phobius(data, ...)

Arguments

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 SeqFastaAA resulting from read.fasta call. Alternatively an AAStringSet object. Should be left blank if vectors are provided to sequence and id arguments.
...	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.

Details

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 /.

Value

A data frame with columns:

id

Character, name of the submitted sequence.

tm

Integer, the number of predicted transmembrane segments.

sp

Character, Y/0 indicator if a signal peptide was predicted or not.

prediction

Character string, predicted topology of the protein.

cut_site

Integer, first amino acid after removal of the signal peptide

is.phobius

Logical, did Phobius predict the presence of a signal peptide

sp.length

Integer, length of the predicted signal peptide.

Note

This function creates temporary files in the working directory.

Source

http://phobius.sbc.su.se/

References

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

See Also

get_signalp

Examples

library(ragp)
data(at_nsp)

phobius_pred <- get_phobius(at_nsp[1:20,],
                            sequence,
                            Transcript.id)
phobius_pred

missuse/ragp documentation built on Jan. 4, 2022, 10:49 a.m.