Workflow Entry: BLAST-ClustalW workflow
Created at: 13/05/10 @ 02:11:12
Last updated: 13/05/10 @ 02:12:28
 Version 1
(of 1)
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Title:
BLAST-ClustalW workflow
Type:
Taverna 2
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Description
Execute blastn against DDBJ database with a given DNA sequence and compare the alignment regions of high similar sequences by using ClustalW.
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Workflow Components
Authors (2)
Titles (2)
| REST access of xml.nig.ac.jp |
| Blast-ClustalW workflow |
Descriptions (2)
|
| See http://xml.nig.ac.jp/tutorial/rest/index.html and http://xml.nig.ac.jp/index.html#services
This workflow has a beanshell script for composing the REST URL for the service at xml.nig.ac.jp.
The example invokes the getDDBJEntry(accession) method of the getEntry service at http://xml.nig.ac.jp/wabi/Method?serviceName=GetEntry&mode=methodList&lang=en - but the workflow can be modified to invoke any other service from http://xml.nig.ac.jp/index.html#services by modifying the "service" and "method" parameters to compose_URL.
Any other input parameters to compose_URL are added to the URL as well, so if instead you want to invoke the method "analyzeParamAsync(query, param)" from the "ClustalW" service, first modify the "service" and "method" default parameters to "ClustalW" and "analyzeParamAsync", and then edit the beanshell script's input ports: Remove the "accession" port from compose_URL, then add "query" and "param". You don't need to modify the actual beanshell script as it picks up any declared input parameters.
This pattern could probably be used for many REST services that work like xml.nig.ac.jp - but the disadvantage is that one has to manually read the documentations to figure out what the parameters are to be. |
Inputs (1)
| Name |
Description |
| 16S_rRNA |
|
Processors (11)
| Name |
Type |
Description |
| Get_BLAST_result_by_Blast_searchParam |
localworker |
|
| Make_query_for_BLAST_against_DDBJ_bacteria_division |
beanshell |
|
| Split_string_BLAST_result_by_enter |
localworker |
|
| Split_string_enter |
stringconstant |
|
| database |
stringconstant |
|
| Parse_BLAST_result |
beanshell |
|
| Make_query_for_retrieving_flatfile |
beanshell |
|
| Get_aligned_sequences_of_subject_entries_by_GetEntry_getDDBJEntry |
localworker |
|
| Extract_aligned_dna_sequences_from_previous_entry |
beanshell |
|
| Execute_ClustalW |
beanshell |
|
| param |
stringconstant |
|
Beanshells (5)
| Name |
Description |
Inputs |
Outputs |
| Make_query_for_BLAST_against_DDBJ_bacteria_division |
|
database
query
param
|
url
|
| Parse_BLAST_result |
|
blastresult
|
accessionlist
startList
endList
|
| Make_query_for_retrieving_flatfile |
|
accession
|
url
|
| Extract_aligned_dna_sequences_from_previous_entry |
|
entryList
startList
endList
|
entry
|
| Execute_ClustalW |
|
entry
query
|
output
|
Datalinks (15)
| Source |
Sink |
| Make_query_for_BLAST_against_DDBJ_bacteria_division:url |
Get_BLAST_result_by_Blast_searchParam:url |
| database:value |
Make_query_for_BLAST_against_DDBJ_bacteria_division:database |
| param:value |
Make_query_for_BLAST_against_DDBJ_bacteria_division:param |
| 16S_rRNA |
Make_query_for_BLAST_against_DDBJ_bacteria_division:query |
| Split_string_enter:value |
Split_string_BLAST_result_by_enter:regex |
| Get_BLAST_result_by_Blast_searchParam:contents |
Split_string_BLAST_result_by_enter:string |
| Split_string_BLAST_result_by_enter:split |
Parse_BLAST_result:blastresult |
| Parse_BLAST_result:accessionlist |
Make_query_for_retrieving_flatfile:accession |
| Make_query_for_retrieving_flatfile:url |
Get_aligned_sequences_of_subject_entries_by_GetEntry_getDDBJEntry:url |
| Get_aligned_sequences_of_subject_entries_by_GetEntry_getDDBJEntry:contents |
Extract_aligned_dna_sequences_from_previous_entry:entryList |
| Parse_BLAST_result:endList |
Extract_aligned_dna_sequences_from_previous_entry:endList |
| Parse_BLAST_result:startList |
Extract_aligned_dna_sequences_from_previous_entry:startList |
| Extract_aligned_dna_sequences_from_previous_entry:entry |
Execute_ClustalW:entry |
| 16S_rRNA |
Execute_ClustalW:query |
| Execute_ClustalW:output |
Result |
Coordinations (2)
| Controller |
Target |
| Get_aligned_sequences_of_subject_entries_by_GetEntry_getDDBJEntry |
Extract_aligned_dna_sequences_from_previous_entry |
| Extract_aligned_dna_sequences_from_previous_entry |
Execute_ClustalW |
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