get_tmhmm: Query TMHMM-2.0 web server.

In missuse/ragp: Mining for Hydroxyproline rich glycoprotein sequences

Description

TMHMM server offers prediction of transmembrane helices in proteins

Usage

get_tmhmm(data, ...)

## S3 method for class 'character'
get_tmhmm(data, splitter = 2500L, attempts = 2, progress = FALSE, ...)

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

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

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

## S3 method for class 'AAStringSet'
get_tmhmm(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.
splitter	An integer indicating the number of sequences to be in each .fasta file that is to be sent to the server. Default is 2500. Change only in case of a server side error. Accepted values are in range of 1 to 10000.
attempts	Integer, number of attempts if server unresponsive, at default set to 2.
progress	Boolean, whether to show messages of the job id for each batch. Default is 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.

Value

A data frame with columns:

id

Character, name of the submitted sequence.

length

Integer, length of the protein sequence

ExpAA

Numeric, the expected number of amino acids in transmembrane helices.

First60

Numeric, the expected number of amino acids in transmembrane helices in the first 60 amino acids of the protein.

tm

Integer, the number of predicted transmembrane segments.

prediction

Character string, predicted topology of the protein.

Note

This function creates temporary files in the working directory. If something goes wrong during communication with the server and progress was set to TRUE, predictions can be obtained using the web address 'paste("https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=", jobid, "&wait=20", sep = "")'.

Source

https://services.healthtech.dtu.dk/service.php?TMHMM-2.0

References

Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305(3):567-80.

See Also

get_phobius

Examples

library(ragp)
tmhmm_pred <- get_tmhmm(data = at_nsp[1:10,],
                        sequence,
                        Transcript.id)
tmhmm_pred

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