Blast_and_Interproscan

Created: 2013-01-28 10:07:16 Last updated: 2013-01-30 12:45:33

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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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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (2)

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).
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

Processors (28)

Name	Type	Description
run	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl Wsdl Operation run
run_input	xmlsplitter
run_output	xmlsplitter
run_input_2	xmlsplitter
Status	workflow
program_value	stringconstant	Value blastp
database_value	stringconstant	Value uniprotkb
stype_value	stringconstant	Value protein
getResult	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl Wsdl Operation getResult
getResult_originalFormat	xmlsplitter
getResult_output	xmlsplitter
output_out	stringconstant	Value out
getResult_graphic	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl Wsdl Operation getResult
getResult_graphicFormat	xmlsplitter
getResult_graphic_output	xmlsplitter
output_visual	stringconstant	Value visual-png
getResult_IDlist	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl Wsdl Operation getResult
getResult_IDListFormat	xmlsplitter
getResult_IDList_output	xmlsplitter
output_ids	stringconstant	Value ids
scores_value	stringconstant	Value 10
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
Filter_IDs	localworker	Script import 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)); } }
Split_IDs	localworker	Script List 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]); } }
regex_value	stringconstant	Value \n
group_value	stringconstant	Value 0
MatchPattern	stringconstant	Value [A-Z_0-9]{4,}_*.

Beanshells (0)

Outputs (5)

Name	Description
getStatus_output_status
getResult_original_output
getResult_graphic_output_output
getResult_2_output_output
InterproScan_Example_Graphical_output

Datalinks (35)

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
Status:getStatus_output_status	getStatus_output_status
getResult_output:output	getResult_original_output
getResult_graphic_output:output	getResult_graphic_output_output
getResult_IDList_output:output	getResult_2_output_output
InterproScan:Graphical_output	InterproScan_Example_Graphical_output

Coordinations (3)

Controller	Target
Status	getResult_originalFormat
Status	getResult_IDListFormat
Status	getResult_graphicFormat

Information Workflow Type

Taverna 2

Information Uploader

Katy Wolstencroft

Information License

All versions of this Workflow are licensed under:

Information Version 3 (of 5)

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Katy Wolstencroft

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Information Statistics

3401 viewings

1494 downloads

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Citations (0)

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Version History

In chronological order:

Blast_and_Interproscan

Created by Katy Wolstencroft on Monday 28 January 2013 10:07:16 (UTC)
Blast_and_Interproscan

Created by Katy Wolstencroft on Tuesday 29 January 2013 12:10:19 (UTC)
Blast_and_Interproscan

Created by Katy Wolstencroft on Tuesday 29 January 2013 12:13:51 (UTC)
Blast_and_Interproscan

Created by Katy Wolstencroft on Wednesday 30 January 2013 12:34:48 (UTC)
Blast_and_Interproscan

Created by Katy Wolstencroft on Wednesday 30 January 2013 12:45:33 (UTC)

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Taverna 2

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Hamish McWilliam

NCBI BLAST (SOAP) (1)

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Perform a BLAST search using the EMBL-EBIâ€™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.