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Tag: BLAST Licence: by-sa

Workflow Workflow for Protein Sequence Analysis (1)

This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.

Created: 2008-01-09 | Last updated: 2008-01-09

Credits: User M.B.Monteiro

Attributions: Workflow BLAST using DDBJ service Workflow Simplify a BLAST text file Workflow conditional branch


Workflow Mapping OligoNucleotides to an assembly (7)

Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

Created: 2009-02-13 | Last updated: 2009-02-13

Credits: User Wassinki User Pieter Neerincx

Attributions: Workflow Blat against ENSEMBLE Danio_rerio_Genome Workflow BlatBlastCombi Workflow Blast against ENSEMBLE Danio_rerio_Genome Workflow AppendToFile Blob Test Input for Mapping oligonucleotides to an assembly Blob Input for Mapping oligonucleotides to an assembly


Workflow fetchEnsemblSeqsAndBlast (1)

This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

Created: 2008-04-18 | Last updated: 2008-04-18

Credits: User Bela

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 Nucleotide InterProScan for the BioExtract... (3)

This workflow can be downloaded and imported into the BioExtract Server at This workflow is a BioExtract Server process similar to the Nucleotide InterProScan workflow designed and implement in Taverna by Hamish McWilliams. The InterProScan tool ( searches a protein sequence against a selection of protein domain, feature and family signature databases, and integrates the results giving potential assignments to InterPro entries and Gen...

Created: 2009-04-16 | Last updated: 2009-07-01

Credits: User Carol Lushbough User Hamish McWilliam

Attributions: Workflow Nucleotide_InterProScan

Workflow Retrieve Protein Sequence and BLAST (1)

Retrieves a protein sequence in Fasta format from Genbank and then performs a BLAST on that sequence

Created: 2007-11-09 | Last updated: 2008-06-05

Credits: User Katy Wolstencroft


Workflow BlatBlastCombi (2)

This workflow combines the blat and blast workflows. It takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and and a set of Fasta sequences. It first tries to perform a blat (at When this service returns nothing, a blast is done (also at The resulting reports are combined.   To run this workflow, a certificate to access needs to installed (Some services use an SSL connection). Look at the ...

Created: 2009-02-03 | Last updated: 2009-02-03

Credits: User Wassinki


Workflow Blast against ENSEMBLE Danio_rerio_Genome (1)

This workflow invokes the blast service provided at, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report.   To run this workflow, a certificate to access needs to installed (Some services use an SSL connection). Look at the link below how to ins...

Created: 2008-10-15 | Last updated: 2008-10-15

Credits: User Wassinki

Workflow EBI_NCBI_BLAST (4)

This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. This workflow uses the new EBI services. They are asynchronous and so require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now wo...

Created: 2011-01-17 | Last updated: 2013-05-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST


Workflow Multi sequences NCBI BLAST (1)

Run a BLAST analysis using the EBI's WSNCBIBlast service (see This workflow wraps the EBI_NCBI_BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence file, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default.

Created: 2008-12-05

Credits: User Whybiocc

Attributions: Workflow EBI_NCBI_BLAST Workflow EBI_NCBI_BLAST_with_prompts Workflow EBI_Blast2InterPro

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