TMHMM server offers prediction of transmembrane helices in proteins
get_tmhmm(data, ...) # S3 method for character get_tmhmm(data, splitter = 2500L, attempts = 2, progress = FALSE, ...) # S3 method for data.frame get_tmhmm(data, sequence, id, ...) # S3 method for list get_tmhmm(data, ...) # S3 method for default get_tmhmm(data = NULL, sequence, id, ...) # S3 method for AAStringSet get_tmhmm(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 |
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... | 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. |
https://services.healthtech.dtu.dk/service.php?TMHMM-2.0
A data frame with columns:
Character, name of the submitted sequence.
Integer, length of the protein sequence
Numeric, the expected number of amino acids in transmembrane helices.
Numeric, the expected number of amino acids in transmembrane helices in the first 60 amino acids of the protein.
Integer, the number of predicted transmembrane segments.
Character string, predicted topology of the protein.
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 = "")`.
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.
#> id length ExpAA First60 tm prediction #> 1 ATCG00660.1 117 12.93 0.59 0 i #> 2 AT2G43600.1 273 6.17 6.13 0 o #> 3 AT2G28410.1 115 12.94 9.53 0 o #> 4 AT2G22960.1 184 0.01 0.01 0 o #> 5 AT2G19580.1 270 90.00 41.19 4 i9-31o41-63i70-92o231-253i #> 6 AT2G19690.2 148 21.89 19.81 1 i7-26o #> 7 AT2G19690.1 147 20.76 19.79 1 i7-26o #> 8 AT2G33130.1 103 20.43 20.43 1 i7-26o #> 9 AT2G05520.1 145 20.20 20.20 1 i7-29o #> 10 AT2G05520.2 138 20.28 20.27 1 i7-29o