The Phobius tool predicts transmembrane domains and signal peptide region from a protein sequence. This workflow uses the EBI's WSPhobius web service (see http://www.ebi.ac.uk/Tools/webservices/services/phobius) to access the tool. The predicted features are returned in a UniProtKB style feature listing.
Wrap input data in a list.
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Submit a Phobius analysis job
(see http://www.ebi.ac.uk/Tools/webservices/services/phobius#runphobius_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSPhobius.wsdl
runPhobius
Parameters for the job. Set to give UniProtKB style features as output.
long
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Add a type to the input data.
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Unpack byte[] recived into a string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Wait until the job has finished and get the specified type of result data.
(see http://www.ebi.ac.uk/Tools/webservices/services/phobius#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSPhobius.wsdl
poll
Check for job completion.
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
Get the status of a submited job
(see http://www.ebi.ac.uk/Tools/webservices/services/phobius#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSPhobius.wsdl
checkStatus
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
import java.util.StringTokenizer;
// GFF format document
phobius_gff = "";
// Sequence ID
seqId = "";
// Break input into lines.
StringTokenizer tok1 = new StringTokenizer(phobius_output, "\n");
while(tok1.hasMoreElements()) {
line = tok1.nextElement();
if(line.startsWith("ID ")) {
seqId = line.substring(5);
}
else if(line.startsWith("FT ")) {
phobius_gff += seqId + "\tPhobius";
StringTokenizer tok2 = new StringTokenizer(line);
fieldCount = 0;
while(tok2.hasMoreElements()) {
fieldStr = tok2.nextElement();
fieldCount++;
if(fieldCount > 1 && fieldCount < 4) {
phobius_gff += "\t" + fieldStr;
}
else if(fieldCount == 4) { // Stop coord
phobius_gff += "\t" + fieldStr + "\t.\t.\t.\t";
}
else if(fieldCount > 4) {
phobius_gff += fieldStr + " ";
}
}
phobius_gff += "\n";
}
}
phobius_output
phobius_gff
User e-mail address.
Protein sequence to analyse. Either the actual sequence (fasta format recommended) or an entry identifer in database:identifer format (e.g. uniprot:LPHN2_RAT).
EBI job identifier.
Predicted features in a UniProtKB style format.
Completed
EBI_Phobius_poll_job
Get_text_result
Scheduled
Running