The CENSOR tool identifies and masks simple and complex sequence repeats found in nucleotide and protein sequences. This workflow uses the EBI's WSCensor web service (see http://www.ebi.ac.uk/Tools/webservices/services/censor) to access the tool.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Submit a CENSOR analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#runcensor_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSCensor.wsdl
runCensor
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
toolaln
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSCensor.wsdl
poll
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
toolmap
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSCensor.wsdl
poll
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSCensor.wsdl
poll
Check status of a WSCensor job.
Check status of a WSCensor job.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
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/censor#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSCensor.wsdl
checkStatus
User e-mail address.
Input sequence. Either an actual sequence (fasta format recommended) or an entry identifier in database:identifier format (e.g. embl:AJ608703).
Library of complex repeats to search against (e.g. Fungi).
Repeat masked sequence in fasta format.
Alignments of the repeat signature sequences with the masked regions.
Table describing maksed regions and identified repeats.
Completed
EBI_CENSOR_poll_job
Get_masked_sequence
Scheduled
Running
Completed
EBI_CENSOR_poll_job
Get_alignment
Scheduled
Running
Completed
EBI_CENSOR_poll_job
Get_table
Scheduled
Running