blastn and blastx

Created: 2011-06-08 15:24:57 Last updated: 2011-06-08 15:37:27

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This workflow accepts an url of a fasta file as input and performs an NCBI blastn at the EBI against the bacteria database and an NCBI blastx against the uniref90 database.

From the blast results of the blastx the hit with the lowest e-value is taken and the GO is returned.

Output is blastx and blastn results and GO from the first hit of the blastx.

Based on Katy Wolstencroft & Hamish McWilliam EBI_NCBI_BLAST http://www.myexperiment.org/workflows/1765.html

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Workflow Components

Authors (2)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
file_url

Processors (44)

Name	Type	Description
run_blastx	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl Wsdl Operation run
run_input	xmlsplitter
run_output	xmlsplitter
Status	workflow
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
run_input_2	xmlsplitter
Fasta_file_parser	workflow
uniref90	stringconstant	Value uniref90
blastx	stringconstant	Value blastx
email_value	stringconstant	Value nep@hotmail.com
dna2	stringconstant	Value dna
run_blastn	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl Wsdl Operation run
run_input_3	xmlsplitter
run_output_2	xmlsplitter
Status_2	workflow
getResult_2	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl Wsdl Operation getResult
getResult_originalFormat_2	xmlsplitter
getResult_output_2	xmlsplitter
output_out_2	stringconstant	Value out
getResult_graphic_2	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl Wsdl Operation getResult
getResult_graphicFormat_2	xmlsplitter
getResult_graphic_output_2	xmlsplitter
output_visual_2	stringconstant	Value visual-png
getResult_IDlist_2	wsdl	Wsdl http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdl Wsdl Operation getResult
getResult_IDListFormat_2	xmlsplitter
getResult_IDList_output_2	xmlsplitter
output_ids_2	stringconstant	Value ids
run_input_2_2	xmlsplitter
em_rel_std_pro	stringconstant	Value em_rel_std_pro
blastn	stringconstant	Value blastn
dna	stringconstant	Value dna
get_gi	beanshell	Script import java.util.regex.; String [] lines = in1.split("\n"); List list = new ArrayList(); Pattern p = Pattern.compile("(UniRef90_)."); String result = ""; for (int i =0;i
KEGG_Pathways_and_Additional_Information	workflow

Beanshells (5)

Name	Inputs	Outputs
get_gi	in1	out1
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
GO_deXMLer	in1	out1
String_to_list	in1	out1
Take_fasta	in1	out1

Outputs (10)

Name	Description
getStatus_status_blastx
getResult_original_output_blastx
getResult_graphic_output_blastx
getResult_output_blastx
getStatus_output_status_blastn
getResult_original_output_blastn
getResult_graphic_output_output_blastn
getResult_2_output_output_blastn
GI_out
GO_output

Datalinks (55)

Source	Sink
run_input:output	run_blastx:parameters
run_input_2:output	run_input:parameters
email_value:value	run_input:email
run_blastx:parameters	run_output:input
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
Fasta_file_parser:fasta_list	run_input_2:sequence
uniref90:value	run_input_2:database
blastx:value	run_input_2:program
dna2:value	run_input_2:stype
file_url	Fasta_file_parser:file_url
run_input_3:output	run_blastn:parameters
run_input_2_2:output	run_input_3:parameters
email_value:value	run_input_3:email
run_blastn:parameters	run_output_2:input
run_output_2:jobId	Status_2:jobID
getResult_originalFormat_2:output	getResult_2:parameters
run_output_2:jobId	getResult_originalFormat_2:jobId
output_out_2:value	getResult_originalFormat_2:type
getResult_2:parameters	getResult_output_2:input
getResult_graphicFormat_2:output	getResult_graphic_2:parameters
run_output_2:jobId	getResult_graphicFormat_2:jobId
output_visual_2:value	getResult_graphicFormat_2:type
getResult_graphic_2:parameters	getResult_graphic_output_2:input
getResult_IDListFormat_2:output	getResult_IDlist_2:parameters
run_output_2:jobId	getResult_IDListFormat_2:jobId
output_ids_2:value	getResult_IDListFormat_2:type
getResult_IDlist_2:parameters	getResult_IDList_output_2:input
em_rel_std_pro:value	run_input_2_2:database
blastn:value	run_input_2_2:program
dna:value	run_input_2_2:stype
Fasta_file_parser:fasta_list	run_input_2_2:sequence
getResult_IDList_output:output	get_gi:in1
get_gi:out1	KEGG_Pathways_and_Additional_Information:gi_ID
Status:getStatus_output_status	getStatus_status_blastx
getResult_output:output	getResult_original_output_blastx
getResult_graphic_output:output	getResult_graphic_output_blastx
getResult_IDList_output:output	getResult_output_blastx
Status_2:getStatus_output_status	getStatus_output_status_blastn
getResult_output_2:output	getResult_original_output_blastn
getResult_graphic_output_2:output	getResult_graphic_output_output_blastn
getResult_IDList_output_2:output	getResult_2_output_output_blastn
get_gi:out1	GI_out
KEGG_Pathways_and_Additional_Information:GO_output	GO_output

Coordinations (6)

Controller	Target
Status	getResult_graphicFormat
Status	getResult_IDListFormat
Status_2	getResult_IDListFormat_2
Status_2	getResult_originalFormat_2
Status_2	getResult_graphicFormat_2
Status	getResult_originalFormat

Information Workflow Type

Taverna 2

Information Uploader

Niek

Information License

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Information Version 1 (of 1)

Information Credits (1)

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Niek

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None

Information Tags (1)

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blastx blastn blast go

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Information Statistics

1755 viewings

1320 downloads

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Version History

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blastn and blastx

Created by Niek on Wednesday 08 June 2011 15:24:57 (UTC)

Last edited by Niek on Wednesday 08 June 2011 15:37:27 (UTC)

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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.

Created: 2010-11-29 | Last updated: 2013-03-28

Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP)

blastn and blastx

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