EBI_dbfetch_fetchBatch

Created: 2008-05-31 20:59:46

Download Workflow

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).

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/209/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
ID_list	List of entry identifers from a specific database.
Database	Name of the database to which the identifiers belong. For example "uniprot".

Processors (2)

Name	Type	Description
fetchBatch	arbitrarywsdl	Get a set of database entries (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch#fetchbatch_db_ids_format_style)
Format_list_for_dbfetch	local	Reformat the list of identifiers into a comma-delimited string for use with fetchBatch.

Beanshells (0)

Outputs (1)

Name	Description
Sequences	Set of sequences in fasta format.

Links (4)

Source	Sink
Database	fetchBatch:db
ID_list	Format_list_for_dbfetch:stringlist
Format_list_for_dbfetch:concatenated	fetchBatch:ids
fetchBatch:fetchBatchReturn	Sequences

Coordinations (0)

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 (3)

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

3599 viewings

2513 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

EBI_dbfetch_fetchBatch

Created by Hamish McWilliam on Saturday 31 May 2008 20:59:46 (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

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

Taverna 1

Uploader

Hamish McWilliam

Protein_alignment_transmembrane (1)

Download

Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: Sequence similarity search (SSS) to find homologues Fetch sequences of hits Multiple sequence alignment (MSA) of hit sequences EMBOSS tmap with alignment from 3. Uses the EBI web services: WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/servic...

Created: 2008-06-01

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch