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Creator:

Carol Lushbough

BioExtract Server Workflow Tutorial

Created: 07/08/09 @ 16:04:23 | Last updated: 07/08/09 @ 16:23:53

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Uploader:

Carol Lushbough

BioExtract Server Workflow Tutorial

Created: 07/08/09 @ 16:20:06 | Last updated: 07/08/09 @ 16:25:46

Credits: Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word 2007 document

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Original Uploader

Hamish McWilliam

EBI_ClustalW2 (v2)

Created: 07/04/09 @ 20:06:03

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Perform a ClustalW multiple sequence alignment using the EBI’s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default.

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Original Uploader

Hamish McWilliam

Protein_search_fetch_align_tree (v2)

Created: 07/04/09 @ 20:13:19

Credits: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

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...

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Original Uploader

Hamish McWilliam

EBI_Kalign (v1)

Created: 02/06/08 @ 21:28:56

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default.

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Original Uploader

Hamish McWilliam

EBI_MUSCLE (v1)

Created: 03/06/08 @ 06:16:22

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

Perform a multiple sequence alignment using the MUSCLE tool (see http://www.drive5.com/muscle/). The EBI's WSMuscle web service (see http://www.ebi.ac.uk/Tools/webservices/services/muscle) is used.

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Original Uploader

Steffen Möller

mustang provides structural alignment of two proteins (v3)

Created: 20/08/08 @ 14:41:21 | Last updated: 25/08/08 @ 15:40:45

Credits: Steffen Möller

Attributions: Fetch PDB flatfile from RCSB server

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow experiments with the partial execution of jobs on a computational grid. The workflow elements "mustang" and "boxshade" are executed on grid nodes. Access to these resources is orchestrated with the plugin available on http://grid.inb.uni-luebeck.de. Please contact the author of this workflow for access permissions.

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Original Uploader

Youguru...

SH2 domain screen in homo (v1)

Created: 19/02/09 @ 16:34:22 | Last updated: 08/06/09 @ 10:30:49

Credits: Youguruozhu

License: Creative Commons Attribution-Share Alike 3.0 Unported License

You can now Download this Workflow and import it into BioExtract Server at bioextract.org. This workflow retrieves a set of protein sequences containing SH2 domain in homo sapiens from NCBI GenBank Protein, then extracts the sequences of SH2 regions and performs a multiple alignment using EMMA and ClustalW. The alignment by EMMA is then plotted to PNG images, simultaneously creating a frequency matrix by prophecy. Finally scan a protein sequence queried with the frequency matrix using prophet.

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Original Uploader

Carol Lushbough

NCBI tblastx non-redundant alignment (v2)

Created: 16/09/09 @ 18:00:09 | Last updated: 25/02/10 @ 19:40:25

Credits: Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow may be downloaded and imported into the BioExtract Server at bioextract.org.  Once imported, input and/or parameter setting can be easily modified. This workflow executes NCBI tblastx on a sequence provided by the user. It then saves the results as a searchable data extract, executes xmknr to remove duplicate sequences,  and performs a clustal alignment on the CDS protein translations.

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Original Uploader

Katy Wolstencroft

BioMart and Emboss Analysis (T2) (v1)

Created: 15/09/09 @ 15:05:11

Credits: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the Taverna 2 version of the Biomart and Emboss Analysis workflow http://www.myexperiment.org/workflows/158   Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the numbe...

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Original Uploader

Achille Zappa

M_Fetch_e-T_phylo_boot - (BETA) (v1)

Created: 10/03/10 @ 15:44:02 | Last updated: 10/03/10 @ 15:49:06

Credits: Achille Zappa Hamish McWilliam

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

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