Perform a Smith-Waterman sequence similarity search using the ScanPS tool (see http://www.compbio.dundee.ac.uk/Software/Scanps/scanps.html). In the case the EBI's WSScanPS web service (see http://www.ebi.ac.uk/Tools/webservices/services/scanps) is used to run the tool.
Submit a ScanPS analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/scanps#runscanps_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSScanPS.wsdl
runScanPS
Wrap input data in list.
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Add type information to input sequence.
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Parameters for the ScanPS job.
50
10.0
0.015
50
1
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/scanps#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSScanPS.wsdl
poll
Unpack the byte[] returned by the service into a string for display.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Check job status, fails if job not done.
Get the status of a submited job (see http://www.ebi.ac.uk/Tools/webservices/services/scanps#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSScanPS.wsdl
checkStatus
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
User e-mail address.
Query sequence. Either the actual sequence (fasta format recommended) or an entry identifier in database:identifier format (e.g. uniprot:wap_rat).
Protein sequence database to search (e.g. swissprot).
Search mode: 200 (simple) or 202 (affine)
EBI job identifier.
ScanPS search report.
Completed
EBI_ScanPS_poll_job
Get_output
Scheduled
Running