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Tag: bioinformatics

Workflow Simplify a BLAST text file (2)

This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simply pass in the string the SAME as the port name, e.g. seq_id, p, per etc.

Created: 2007-10-03 | Last updated: 2009-07-28

Workflow EBI_PICR_Sequence_to_UniParc_and_InterPro (2)

Given a protein sequence get some information about it: Does this protein sequence occur in any of the protein databases (e.g. UniProtKB, PDB, etc.). Using the PICR web service (see map the sequence to a UniParc identifer. Which entries in the protein databases have this sequence. Using the UniParc database (see a summary of the databases and the entries in those databases which have this s...

Created: 2008-06-08 | Last updated: 2008-06-08

Credits: User Hamish McWilliam

Attributions: Workflow EBI_dbfetch_UniParc Workflow EBI_Fetch_InterPro_Matches_UniParc Workflow EBI_PICR_Sequence_to_ID

Workflow EBI InterProScan (2)

EBI InterProScan. Stop fannying around with BLAST and use InterProScan instead.

Created: 2007-10-03

Workflow EBI_NCBI_BLAST (1)

Perform a BLAST search using the EBI’s WSNCBIBlast service (see The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search (see Job_params) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement NCBI BLA...

Created: 2008-05-31 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Workflow EBI WU-BLAST with program and database sel... (3)

Run a BLAST analysis using the EBI's WSWUBlast service (see This workflow wraps the EBI_WU-BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. The values presented in the selection menus for the program and database are obtained from the service, using the provided me...

Created: 2009-07-04 | Last updated: 2010-12-06

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST

Workflow Retrieve sequence in EMBL format (3)

This workflow retrieves a sequence associated with its features in embl format

Created: 2009-06-17

Credits: User Franck Tanoh User Tomoinn User Stuart Owen

Workflow EBI_ClustalW2_phylogentic_tree (2)

Create a Neighbor-joining phylogenetic tree, with Kimura distance corrections, from a sequence alignment using the EBI's WSClustalW2 service (see

Created: 2009-04-07

Credits: User Hamish McWilliam

Workflow Fetch PDB flatfile from RCSB server (1)

Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Created: 2008-03-05 | Last updated: 2008-03-31

Credits: User Tomoinn

Workflow Multiple Blastp (2)

This is a workflow to automate multiple BLASTp jobs on a large list of protein sequences in FASTA format.

Created: 2007-11-20 | Last updated: 2008-01-10

Credits: User Kieren Lythgow

Workflow tmap_single_sequence (2)

Simple workflow using tmap to find transmembrane regions, using a single sequence as input.

Created: 2008-06-01 | Last updated: 2008-06-02

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID

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