Retrieve Protein Sequence

Created: 2008-07-30 16:36:55 Last updated: 2009-12-03 16:54:02

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Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier.

Example input for this workflow is:

EDL10223.1

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Workflow Components

Inputs (1)

Name	Description
ID

Processors (4)

Name	Type	Description
Get_Protein_FASTA	local
searchSimple	arbitrarywsdl	Execute Blast
database	stringconstant
program	stringconstant

Beanshells (0)

Outputs (2)

Name	Description
protein_sequence
blast_report

Links (6)

Source	Sink
ID	Get_Protein_FASTA:id
Get_Protein_FASTA:outputText	searchSimple:query
database:value	searchSimple:database
program:value	searchSimple:program
Get_Protein_FASTA:outputText	protein_sequence
searchSimple:Result	blast_report

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Information Workflow Type

Taverna 1

Information Uploader

Paul Fisher

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Information Version 1 (of 1)

Information Credits (1)

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Katy Wolstencroft

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NeuroScience Newcastle

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Newcastle NeuroScience

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Information Favourited By (1)

Andrew David King

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2762 downloads

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Retrieve Protein Sequence

Created by Paul Fisher on Wednesday 30 July 2008 16:36:55 (UTC)

Last edited by Paul Fisher on Thursday 03 December 2009 16:54:03 (UTC)

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Comments (1)

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Limingl	Monday 13 July 2009 10:40:45 (UTC)
	it is very nice! but if I want to retrieve the whole protein sequence of some microorganism in fasta formate, for example, Asperigillus Niger, How can i do?

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Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSV...

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BLAST using DDBJ service (2)

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Perform a sequence similarity search using the BLAST algorithm through the DDBJ web service. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNIL SRVLARSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLT NTENTASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEAR LKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDY GDVLRAVEKAATRHSLGLP...

Created: 2007-10-03 | Last updated: 2009-12-03