Blast_and_Interproscan
Created: 2013-01-28 10:07:16
Last updated: 2013-01-30 12:45:33
This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required.
The sequences for the top 10 hits are retrieved from the UniProt database and analysed using InterproScan (also from the EBI) to determine functional domains and motifs in each sequence. The results are shown in a graphical format.
This workflow uses the new EBI services. They are asynchronous and so require looping over the nested workflows (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.
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Workflow Components
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Authors (1)
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Titles (1)
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Descriptions (1)
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| This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required.
The sequences for the top 10 hits are retrieved from the UniProt database and analysed using InterproScan (also from the EBI) to determine functional domains and motifs in each sequence. The results are shown in a graphical format.
This workflow uses the new EBI services. They are asynchronous and so require looping over the nested workflows (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. |
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Dependencies (0)
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Inputs (2)
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| Name |
Description |
| sequence |
Query seqeunce. Either the actual sequence (fasta format recommended) or a database identifer in database:identifier format (e.g. uniprot:wap_rat).
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| email |
Requires a valid email address in order to execute services hosted at the EBI.
The EBI asks for an email address so that they can contact you about:
Problems with the service which affect your jobs.
Scheduled maintenance which affects services you are using.
Deprecation and retirement of a service you are using.
If you use a fake email, the workflow may be cancelled before execution
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Processors (28)
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| Name |
Type |
Description |
| run |
wsdl |
Wsdlhttp://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdlWsdl Operationrun |
| run_input |
xmlsplitter |
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| run_output |
xmlsplitter |
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| run_input_2 |
xmlsplitter |
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| Status |
workflow |
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| program_value |
stringconstant |
Valueblastp |
| database_value |
stringconstant |
Valueuniprotkb |
| stype_value |
stringconstant |
Valueprotein |
| getResult |
wsdl |
Wsdlhttp://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdlWsdl OperationgetResult |
| getResult_originalFormat |
xmlsplitter |
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| getResult_output |
xmlsplitter |
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| output_out |
stringconstant |
Valueout |
| getResult_graphic |
wsdl |
Wsdlhttp://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdlWsdl OperationgetResult |
| getResult_graphicFormat |
xmlsplitter |
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| getResult_graphic_output |
xmlsplitter |
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| output_visual |
stringconstant |
Valuevisual-png |
| getResult_IDlist |
wsdl |
Wsdlhttp://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdlWsdl OperationgetResult |
| getResult_IDListFormat |
xmlsplitter |
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| getResult_IDList_output |
xmlsplitter |
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| output_ids |
stringconstant |
Valueids |
| scores_value |
stringconstant |
Value10 |
| InterproScan |
workflow |
This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png.
This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. |
| REST_UniProt |
rest |
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| Filter_IDs |
localworker |
Scriptimport java.util.regex.*;
filteredlist = new ArrayList();
Pattern thePat = Pattern.compile(regex);
int theGroup = Integer.parseInt(group);
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
Matcher matcher = thePat.matcher(item);
if (matcher.find()) {
filteredlist.add(matcher.group(theGroup));
}
}
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| Split_IDs |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
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| regex_value |
stringconstant |
Value\n |
| group_value |
stringconstant |
Value0 |
| MatchPattern |
stringconstant |
Value[A-Z_0-9]{4,}_*. |
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Beanshells (0)
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Outputs (4)
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| Name |
Description |
| BlastResultText |
Produces a BLAST alignment in flat-file format
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| BlastResultGraphic |
Produces a BLAST alignment in graphical format
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| InterproScanGraphical |
Produces a graphical representation of InterproScan matches against a protein sequence.
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| status_blast |
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Datalinks (34)
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| Source |
Sink |
| run_input:output |
run:parameters |
| run_input_2:output |
run_input:parameters |
| email |
run_input:email |
| run:parameters |
run_output:input |
| sequence |
run_input_2:sequence |
| program_value:value |
run_input_2:program |
| database_value:value |
run_input_2:database |
| stype_value:value |
run_input_2:stype |
| scores_value:value |
run_input_2:scores |
| run_output:jobId |
Status:jobID |
| getResult_originalFormat:output |
getResult:parameters |
| run_output:jobId |
getResult_originalFormat:jobId |
| output_out:value |
getResult_originalFormat:type |
| getResult:parameters |
getResult_output:input |
| getResult_graphicFormat:output |
getResult_graphic:parameters |
| run_output:jobId |
getResult_graphicFormat:jobId |
| output_visual:value |
getResult_graphicFormat:type |
| getResult_graphic:parameters |
getResult_graphic_output:input |
| getResult_IDListFormat:output |
getResult_IDlist:parameters |
| run_output:jobId |
getResult_IDListFormat:jobId |
| output_ids:value |
getResult_IDListFormat:type |
| getResult_IDlist:parameters |
getResult_IDList_output:input |
| REST_UniProt:responseBody |
InterproScan:sequence |
| email |
InterproScan:email |
| Filter_IDs:filteredlist |
REST_UniProt:id |
| Split_IDs:split |
Filter_IDs:stringlist |
| group_value:value |
Filter_IDs:group |
| MatchPattern:value |
Filter_IDs:regex |
| getResult_IDList_output:output |
Split_IDs:string |
| regex_value:value |
Split_IDs:regex |
| getResult_output:output |
BlastResultText |
| getResult_graphic_output:output |
BlastResultGraphic |
| InterproScan:Graphical_output |
InterproScanGraphical |
| Status:getStatus_output_status |
status_blast |
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Coordinations (3)
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| Controller |
Target |
| Status |
getResult_graphicFormat |
| Status |
getResult_IDListFormat |
| Status |
getResult_originalFormat |
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NCBI BLAST (SOAP)
(1)
Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.
Created: 2010-11-29
| Last updated: 2013-03-28
Attributions:
EBI_NCBI_BLAST
NCBI BLAST (SOAP)
NCBI BLAST (SOAP)
(1)
Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.
Created: 2010-11-29
| Last updated: 2013-03-28
Credits:
Hamish McWilliam
Attributions:
EBI_NCBI_BLAST
NCBI BLAST (SOAP)
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