Run a FASTA analysis using the EBI’s WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). This workflow wraps the EBI_FASTA workflow to provide a basic user interface which prompts for the required inputs: sequence, database, FASTA program and user e-mail. Other parameters (e.g. matrix, gap penalties, etc.) are allowed to default.
List of available databases.
embl,uniprot,pdb
,
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
Select the required database.
Database
Database
net.sourceforge.taverna.scuflworkers.ui.SelectWorker
Select the required FASTA program.
Program
FASTA Program
net.sourceforge.taverna.scuflworkers.ui.SelectWorker
List of available FASTA programs.
fasta3,fastf3,fasts3,fastx3,fasty3,tfastx3,tfasty3,ssearch
,
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
Ask for the user's e-mail address.
E-mail
Your e-mail
net.sourceforge.taverna.scuflworkers.ui.AskWorker
Ask for the query sequence, either as a sequence identifier in database:identifer format (e.g. uniprot:wap_rat) or the actual sequence (fasta format recommended).
Query sequence
Sequence or ID
net.sourceforge.taverna.scuflworkers.ui.AskWorker
Run a FASTA or SSEARCH sequence similarity search using the EBI's WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta).
Submit the FASTA/SSEARCH job.
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl
runFasta
Input data structure, adds a type to the input sequence.
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Unpack XML FASTA report from byte[] into string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Unpack plain text FASTA report from byte[] into string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Get the hit identifers.
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl
getIds
Wrap the input sequence in a list.
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Get the FASTA report as XML.
toolxml
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl
poll
Get the FASTA report as text.
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl
poll
Parameters for the FASTA/SSEARCH job.
50
50
1.0
0.0
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Check for job completion.
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl
checkStatus
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
Query sequence (fasta format recommended) or sequence identifer in database:identifer format (e.g. uniprot:wap_rat).
The database to search (e.g. uniprot).
Your e-mail address.
The FASTA program to run (e.g. fasta3, fastf3, fasts3, fastx3, fasty3, tfastx, tfasty).
FASTA program output as plain text. Note the exact format of the output depends on the chosen FASTA program.
FASTA output in an XML format.
List of the identifiers of the hits found.
The identifier of the job at EBI.
Completed
Poll_FASTA_Job
getIds
Scheduled
Running
Completed
Poll_FASTA_Job
Get_Text_Result
Scheduled
Running
Completed
Poll_FASTA_Job
Get_XML_Result
Scheduled
Running
Plain text FASTA report.