EBI_Kalign
Created: 2008-06-02 21:28:56
Last updated: 2010-12-06 11:39:52
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.
Note: the WSKalign service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement Kalign services (REST or SOAP) should be used instead.
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Workflow Components
Inputs (3)
Name |
Description |
Sequences |
Sequences to align (fasta format recommended). |
Email_address |
User e-mail address. |
Molecule_type |
Molecule type: P for protein or N for nucleotide. |
Processors (7)
Name |
Type |
Description |
runKalign |
arbitrarywsdl |
Submit a Kalign analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/kalign#runkalign_params_content) |
Get_alignment |
arbitrarywsdl |
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/kalign#poll_jobid_type) |
Job_params |
local |
|
Contents_list |
local |
|
Input_data |
local |
|
Unpack_alignment |
local |
|
EBI_Kalign_poll_job |
workflow |
|
Beanshells (1)
Name |
Description |
Inputs |
Outputs |
Is_done |
|
job_status
|
is_done
|
Outputs (2)
Name |
Description |
Kalign_alignment |
The alignment in ClustalW style format. |
Kalign_job_id |
EBI job identifier. |
Links (11)
Source |
Sink |
Contents_list:output |
runKalign:content |
Email_address |
Job_params:email |
Input_data:output |
Contents_list:WSArrayofData |
Job_params:output |
runKalign:params |
Sequences |
Input_data:content |
Get_alignment:output |
Unpack_alignment:bytes |
Molecule_type |
Job_params:moltype |
runKalign:jobid |
EBI_Kalign_poll_job:Job_ID |
Unpack_alignment:string |
Kalign_alignment |
runKalign:jobid |
Get_alignment:jobid |
runKalign:jobid |
Kalign_job_id |
Coordinations (1)
Controller |
Target |
EBI_Kalign_poll_job |
Get_alignment |
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