Sequence_or_ID

Created: 2008-06-01 14:15:12

Download Workflow

Given a sequence or sequence entry identifer (e.g. uniprot:wap_rat), return the sequence in fasta format.

If a sequence identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/214/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
Sequence_or_ID	Either an actual sequence or an entry identifer in database:identifier format (e.g. uniprot:wap_rat).

Processors (5)

Name	Type	Description
Is_sequence	beanshell	Return true if the input is a sequence or false if the input is a sequence identifer (e.g. uniprot:wap_rat).
Fail_if_identifer	local	Fails if the workflow input is an identifier (i.e. is an actual sequence).
Fail_if_sequence	local	Fails if the workflow input was a sequence (i.e. is an identifer).
fetchData	arbitrarywsdl	Fetch the sequence in fasta format from the identifer using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).
seqret	soaplabwsdl	Format sequence into fasta format.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_sequence	Return true if the input is a sequence or false if the input is a sequence identifer (e.g. uniprot:wap_rat).	sequence	is_sequence

Outputs (1)

Name	Description
Sequence	Sequence in fasta format.

Links (7)

Source	Sink
Sequence_or_ID	Is_sequence:sequence
Is_sequence:is_sequence	Fail_if_identifer:test
Is_sequence:is_sequence	Fail_if_sequence:test
Sequence_or_ID	fetchData:query
Sequence_or_ID	seqret:sequence_direct_data
fetchData:fetchDataReturn	Sequence
seqret:outseq	Sequence

Coordinations (2)

Controller	Target
Fail_if_sequence	fetchData
Fail_if_identifer	seqret

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (0)

(Workflows/Files)

None

Information Tags (6)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (1)

Private pack

Log in to add to one of your Packs

Information Attributed By (3)

(Workflows/Files)

Information Favourited By (0)

No one

Information Statistics

3431 viewings

2498 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Sequence_or_ID

Created by Hamish McWilliam on Sunday 01 June 2008 14:15:12 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (18)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Hamish McWilliam

EBI_dbfetch_fetchBatch (1)

Download

From a list of sequence entry identifiers and a database name, fetch the sequences in fasta format using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl).

Created: 2008-05-31

Credits: Hamish McWilliam

Taverna 1

Uploader

Hamish McWilliam

Protein_search_fetch_align_tree (2)

Download

An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers...

Created: 2009-04-07

Credits: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST