Use the TMHMM and SignalP methods of InterProScan to perform transmembrane and signal peptide prediction. The EBI's InterProScan web service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan) is used.
Unpack byte[] version of result into a string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
InterProScan job parameters.
tmhmm signalp
0
p
0
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Unpack byte[] version of result into a string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Wrap input data in a list.
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Populate input data structure with input sequence and data type.
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Get the plain text format result.
toolraw
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl
poll
Submit the InterProScan job.
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl
runInterProScan
Wait for the job to complete.
If job has not finished fail the workflow.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
Map status codes into true/false is done flag.
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl
checkStatus
EBI job identifer
Status of job
Get the XML format result.
toolxml
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl
poll
User e-mail address
Input protein sequence for analysis. This can either be the actual sequence (fasta format recommended) or a database identifier in database:identifer format (e.g. uniprot:LPHN2_RAT).
InterProScan result in tab delimited plain text format.
text/xml
InterProScan result in XML format.
EBI job identifier.
Completed
EBI_InterProScan_poll_job
Get_text_result
Scheduled
Running
Completed
EBI_InterProScan_poll_job
Get_XML_result
Scheduled
Running