Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default.
Submit a Kalign analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/kalign#runkalign_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSKalign.wsdl
runKalign
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/kalign#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSKalign.wsdl
poll
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Get the status of a submited job (see http://www.ebi.ac.uk/Tools/webservices/services/kalign#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSKalign.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
Sequences to align (fasta format recommended).
User e-mail address.
Molecule type: P for protein or N for nucleotide.
The alignment in ClustalW style format.
EBI job identifier.
Completed
EBI_Kalign_poll_job
Get_alignment
Scheduled
Running