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Items tagged with "protein" (79)

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Files (9)
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Blob Popfly Blocks for Protein Characteristics and Predic...

Created: 27/11/08 @ 10:20:35 | Last updated: 01/12/08 @ 07:11:27

Credits: User Felicity

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Popfly blocks for Protein Characteristics and Prediction Mashup 3. The mashup can be viewed at: www.popfly.com/users/fsn/Protein%20Characteristics%20and%20Prediction%203

File type: ZIP archive

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 52 times | Downloaded: 18 times

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Blob Popfly Blocks for Protein Characteristics and Predic...

Created: 27/11/08 @ 10:18:47 | Last updated: 01/12/08 @ 07:12:41

Credits: User Felicity

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Popfly blocks for Protein Characteristics and Prediction Mashup 2. The mashup can be viewed at: http://www.popfly.com/users/fsn/Protein%20Characteristics%20and%20Prediction%202

File type: ZIP archive

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 22 times | Downloaded: 13 times

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Blob Popfly Blocks for Protein Characteristics and Predic...

Created: 27/11/08 @ 10:17:41 | Last updated: 01/12/08 @ 07:13:40

Credits: User Felicity

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Popfly blocks for Protein Characteristics and Prediction Mashup 1. The mashup can be viewed at: http://www.popfly.com/users/fsn/Protein%20Characteristics%20and%20Prediction%201

File type: ZIP archive

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 26 times | Downloaded: 13 times

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Blob Popfly Blocks for Protein Characteristics Mashup 1

Created: 27/11/08 @ 10:11:14 | Last updated: 01/12/08 @ 07:14:32

Credits: User Felicity

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Popfly blocks for Protein Characteristics Mashup 1. The mashup can be viewed at: www.popfly.com/users/fsn/Protein%20Characteristics%20Mashup%201  

File type: ZIP archive

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 25 times | Downloaded: 11 times

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Blob Popfly Blocks for Protein Prediction Mashup 1

Created: 27/11/08 @ 10:13:29 | Last updated: 01/12/08 @ 07:15:28

Credits: User Felicity

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Popfly blocks for Protein Prediction Mashup 1. The mashup can be viewed at: www.popfly.com/users/fsn/Protein%20Prediction%20Mashup%201  

File type: ZIP archive

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 23 times | Downloaded: 19 times

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Blob Popfly Blocks for Protein Prediction Mashup 2

Created: 27/11/08 @ 10:15:10 | Last updated: 01/12/08 @ 07:16:18

Credits: User Felicity

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Popfly blocks for Protein Prediction Mashup 2. The mashup can be viewed at: www.popfly.com/users/fsn/Protein%20Prediction%20Mashup%201

File type: ZIP archive

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 22 times | Downloaded: 13 times

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Blob Protein Analysis Popfly Blocks

Created: 27/11/08 @ 10:03:04 | Last updated: 01/12/08 @ 07:17:33

Credits: User Felicity

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A zip file containing Popfly blocks for protein analysis. It also includes a file explaining the function of each block as well as a list of mashups in which these blocks have been used.

File type: ZIP archive

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Blob BioExtract Server Workflow Tutorial

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

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial demonstrates how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.

File type: Word 2007 document

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Blob Phenotype Concept Profile - Terms

Created: 11/08/09 @ 13:05:07 | Last updated: 11/08/09 @ 13:06:51

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all terms extracted from the phenotype corpus, relating to African trypanosomiasis resistance in the mouse model. These terms were extracted using the following service: http://gopubmed4.biotec.tu-dresden.de/GoPubMedTermGenerationService/services/GoPubMedTermGeneration?wsdl These terms represent the concept profile for the phenotype.

File type: Plain text

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Workflows (69)
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Workflow DiscoverProteinLink (2)

Created: 03/10/07 @ 18:36:12 | Last updated: 15/11/07 @ 09:02:44

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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COMPETITION: For friends only: If you find any two topics that return true positives with this workflow I will buy you a bottle of wine (or equivalent). Terms: if we confirm that the protein was indeed never mentioned together with both input topics in one article, we will publish this together. ---- This workflow implements Swanson's prinicple with services from the AIDA toolbox. It tries to find proteins that link two topics, while they never mentioned together with both topics in ...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 303 times | Downloaded: 65 times

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Workflow BioAID_DiseaseDiscovery_RatHumanMouseUnipr... (4)

Created: 15/12/08 @ 20:46:09 | Last updated: 11/08/11 @ 09:22:23

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...

Rating: 4.0 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 3 | Citations: 0

Viewed: 4266 times | Downloaded: 664 times

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Original Uploader

Workflow ProteinSynonymsToQuery (2)

Created: 03/10/07 @ 18:36:10 | Last updated: 13/11/07 @ 23:47:41

Credits: User Marco Roos User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow uses Martijn Schuemie's protein synonym service to produce synonyms and a new query string from the input query term. The service is limited to proteins, enzymes and genes. An input query that is a boolean string will be split and processed, but the boolean logic of the input query will be lost. Workflow URL: http://rdf.adaptivedisclosure.org/~marco/BioAID/Public/Workflows/BioAID/ProteinSynonymsToQuery.xml

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 175 times | Downloaded: 72 times

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Workflow BioAID_ProteinDiscovery (7)

Created: 10/05/10 @ 16:21:09 | Last updated: 20/03/12 @ 17:16:11

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This protein discovery workflow extracts protein names from documents retrieved from MedLine based on a user Query (cf Apache Lucene syntax). The protein names are filtered by checking if there exists a valid UniProt ID for the given protein name.

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 389 times | Downloaded: 144 times

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Original Uploader

Workflow BioAID_ProteinToDiseases (1)

Created: 14/11/07 @ 12:47:57 | Last updated: 15/11/07 @ 09:00:44

Credits: User Marco Roos User Martijn Schuemie Network-member AID

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow was based on BioAID_DiseaseDiscovery, changes: expects only one protein name, adds protein synonyms). This workflow finds diseases relevant to the query string via the following steps: A user query: a single protein name Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) Retrieve documents: finds relevant documents (abstract+title) based on query Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link proteins ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 197 times | Downloaded: 94 times

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Original Uploader

Workflow Discover_proteins_from_text (2)

Created: 15/11/07 @ 08:58:00 | Last updated: 15/11/07 @ 09:12:34

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow discovers proteins from plain text. It is built around the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 194 times | Downloaded: 71 times

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Original Uploader

Workflow BioAID_Discover_proteins_from_text_plus_sy... (1)

Created: 15/11/07 @ 09:40:24

Credits: User Marco Roos User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow discovers proteins from plain text and adds synonyms using Martijn Schuemie's proteins synonym service. Proteins are discovered with the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 97 times | Downloaded: 2 times

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Workflow Multiple Blastp (2)

Created: 20/11/07 @ 16:58:38 | Last updated: 10/01/08 @ 12:09:38

Credits: User Kieren Lythgow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 517 times | Downloaded: 165 times

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Original Uploader

Workflow Workflow for Protein Sequence Analysis (1)

Created: 09/01/08 @ 12:03:03 | Last updated: 09/01/08 @ 12:31:27

Credits: User M.B.Monteiro

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 4.0 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1795 times | Downloaded: 467 times

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Original Uploader

Workflow BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

Created: 28/05/09 @ 12:21:05

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member AID_myGrid_collaboration

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow finds proteins relevant to the query string via the following steps: A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach; the AIDA serv...

Rating: 0.0 / 5 (0 ratings) | Versions: 11 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 471 times | Downloaded: 173 times

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Original Uploader

Workflow Fetch PDB flatfile from RCSB server (1)

Created: 05/03/08 @ 14:13:24 | Last updated: 31/03/08 @ 16:01:41

Credits: User Tomoinn

License: Creative Commons Attribution 3.0 Unported License

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

Rating: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 307 times | Downloaded: 121 times

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Workflow GBSeq test (2)

Created: 05/03/08 @ 14:15:35 | Last updated: 31/03/08 @ 15:55:09

Credits: User Franck Tanoh

License: Creative Commons Attribution 3.0 Unported License

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 249 times | Downloaded: 93 times

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Original Uploader

Workflow Protein_search_fetch_align_tree (2)

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

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree Workflow EBI_dbfetch_fetchBatch Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 463 times | Downloaded: 154 times

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Workflow EBI_Phobius (2)

Created: 01/06/08 @ 11:08:45 | Last updated: 02/06/08 @ 21:39:06

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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The Phobius tool predicts transmembrane domains and signal peptide region from a protein sequence. This workflow uses the EBI's WSPhobius web service (see http://www.ebi.ac.uk/Tools/webservices/services/phobius) to access the tool. The predicted features are returned in a UniProtKB style feature listing.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 118 times | Downloaded: 66 times

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Workflow EBI_InterProScan_tmhmm_signalp (4)

Created: 26/10/08 @ 20:50:10 | Last updated: 01/04/11 @ 08:56:37

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Use the TMHMM and Signal...

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 219 times | Downloaded: 89 times

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Original Uploader

Workflow Protein_alignment_transmembrane (1)

Created: 01/06/08 @ 12:20:29

Credits: User Hamish McWilliam

Attributions: Workflow EBI_FASTA Workflow EBI_ClustalW2 Workflow EBI_dbfetch_fetchBatch

License: Creative Commons Attribution 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 208 times | Downloaded: 59 times

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Original Uploader

Workflow tmap_single_sequence (2)

Created: 01/06/08 @ 14:27:12 | Last updated: 02/06/08 @ 21:38:13

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 Unported License

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

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 147 times | Downloaded: 45 times

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Original Uploader

Workflow Protein_transmembrane_prediction (2)

Created: 26/10/08 @ 21:16:10 | Last updated: 01/04/11 @ 08:57:10

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan_tmhmm_signalp Workflow EBI_Phobius Workflow tmap_single_sequence

License: Creative Commons Attribution 3.0 Unported License

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Transmembrane and signal...

Rating: 4.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 3 | Citations: 0

Viewed: 406 times | Downloaded: 92 times

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Original Uploader

Workflow EBI_MPsrch (1)

Created: 02/06/08 @ 21:49:11 | Last updated: 06/12/10 @ 10:38:42

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Run a Smith-Waterman sequence search using the EBI’s WSMPsrch service (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch). Note: the WSMPsrch service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services.  

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 71 times | Downloaded: 44 times

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Original Uploader

Workflow EBI_ScanPS (1)

Created: 03/06/08 @ 05:57:09 | Last updated: 06/12/10 @ 10:37:50

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Perform a Smith-Waterman sequence similarity search using the ScanPS tool (see http://www.compbio.dundee.ac.uk/Software/Scanps/scanps.html). In the case the EBI's WSScanPS web service (see http://www.ebi.ac.uk/Tools/webservices/services/scanps) is used to run the tool. Note: the WSScanPS service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services.  

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 69 times | Downloaded: 39 times

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Original Uploader

Workflow EBI_MaxSprout (2)

Created: 05/06/08 @ 21:44:00 | Last updated: 06/06/08 @ 05:58:16

Credits: User Hamish McWilliam

Attributions: Workflow Structure_or_ID

License: Creative Commons Attribution 3.0 Unported License

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Generation of protein backbone and side chain co-ordinates from a C(alpha) trace using the MaxSprout tool. The EBI's WSMaxsprout service (see http://www.ebi.ac.uk/Tools/webservices/services/maxsprout) is used to access the tool.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 65 times | Downloaded: 42 times

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Workflow Structure_or_ID (1)

Created: 06/06/08 @ 05:57:31

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Given a structure or structure entry identifer (e.g. PDB:1crn), return the structure in PDB format. If a structure 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 structure in PDB format. Otherwise the input is assumed to be a formated structure and is passed through to the output.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 748 times | Downloaded: 42 times

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Workflow Nucleotide_InterProScan (4)

Created: 26/10/08 @ 21:10:09 | Last updated: 01/04/11 @ 08:54:21

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow EBI_NCBI_BLAST Workflow Nucleotide_ORF_translation Workflow Fasta_string_to_fasta_list Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 Unported License

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Run InterProScan using a...

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 415 times | Downloaded: 125 times

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Workflow EBI_Blast2InterPro (2)

Created: 26/10/08 @ 20:45:45 | Last updated: 22/08/12 @ 11:22:43

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST Workflow EBI_dbfetch_fetchBatch Workflow Fasta_string_to_fasta_list Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services. Perform a BLAST search a...

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 272 times | Downloaded: 103 times

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Original Uploader

Workflow EBI_DaliLite (1)

Created: 07/06/08 @ 17:16:37

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Pairwise structure comparison using the DaliLite tool. The EBI's WSDaliLite web service (see http://www.ebi.ac.uk/Tools/webservices/services/dalilite) is used to access the tool.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 80 times | Downloaded: 50 times

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Original Uploader

Workflow EBI_PICR_Sequence_to_UniParc_and_InterPro (2)

Created: 08/06/08 @ 13:53:39 | Last updated: 08/06/08 @ 14:10:02

Credits: User Hamish McWilliam

Attributions: Workflow EBI_dbfetch_UniParc Workflow EBI_Fetch_InterPro_Matches_UniParc Workflow EBI_PICR_Sequence_to_ID

License: Creative Commons Attribution 3.0 Unported License

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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 http://www.ebi.ac.uk/Tools/picr/) map the sequence to a UniParc identifer. Which entries in the protein databases have this sequence. Using the UniParc database (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) a summary of the databases and the entries in those databases which have this s...

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 170 times | Downloaded: 60 times

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Workflow EBI_PICR_Sequence_to_ID (1)

Created: 08/06/08 @ 14:03:07

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Map a protein sequence to the known identifiers of identical sequences. Uses the EBI's PICR web service (see http://www.ebi.ac.uk/Tools/picr/) to perform the mapping.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 76 times | Downloaded: 40 times

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Workflow EBI_dbfetch_UniParc (1)

Created: 08/06/08 @ 14:05:40

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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From a list of UniParc entry identifers get the complete entries using the EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 57 times | Downloaded: 34 times

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Workflow EBI_Fetch_InterPro_Matches_UniParc (1)

Created: 08/06/08 @ 14:08:47

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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For a UniParc (see http://www.ebi.ac.uk/uniprot/database/DBDescription.html#uniparc) identifier/accession fetch the assocated InterPro Matches from SRS@EBI (see http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+IPRMC_UNIPARC).

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Workflow EBI_CENSOR (2)

Created: 17/06/08 @ 20:42:46 | Last updated: 25/06/08 @ 06:16:03

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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The CENSOR tool identifies and masks simple and complex sequence repeats found in nucleotide and protein sequences. This workflow uses the EBI's WSCensor web service (see http://www.ebi.ac.uk/Tools/webservices/services/censor) to access the tool.

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Workflow EBI_IntAct (1)

Created: 09/07/08 @ 06:01:17

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Find protein binary interactions using the EBI's IntAct service. See http://www.ebi.ac.uk/intact/ for further details.

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Workflow Retrieve Protein Sequence (1)

Created: 30/07/08 @ 16:36:55 | Last updated: 03/12/09 @ 16:54:02

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1

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Workflow BioAID_EnirchBioModelWithProteinsFromText (7)

Created: 16/05/09 @ 01:06:26 | Last updated: 16/05/09 @ 01:13:18

Credits: User Marco Roos User Sophia katrenko User Andrew Gibson User M. Scott Marshall User Willem van Hage User Edgar User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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This workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you. Summary This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps: it retrieves documents relevant for the query string i...

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Workflow blastp using the MRS system (1)

Created: 28/11/08 @ 15:13:32 | Last updated: 28/11/08 @ 15:34:19

Credits: User Bas Vroling

License: Creative Commons Attribution 3.0 Unported License

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This blastp workflow uses the blast service of MRS (http://mrs.cmbi.ru.nl). Inputs are a sequence (only amino acids, not a fasta sequence) and a database name. Valid database names that can be used are "sprot", "uniprot", "trembl", "pdb", "refseq", "ipi" and "gpcrdb". Output is returned in XML.

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Workflow Using CQL to query protein sequence data (1)

Created: 05/12/08 @ 22:03:03 | Last updated: 14/07/09 @ 19:32:17

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR. Scientific value To query protein sequence information out of 3 caGrid data services: caBIO, CPAS and GridPIR. To analyze a protein sequence from different data sources. Steps Querying CPAS and get the id, name, value of the sequence. Querying caBIO and GridPIR using the id or name obtained from CPAS.    

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Workflow Bio2RDF: Rdfiser for Bind protein interact... (1)

Created: 19/02/09 @ 05:10:23 | Last updated: 19/02/09 @ 05:24:29

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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CONSTRUCT{ <bmuri>, ?p, ?o . } FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { <bmuri>, ?p, ?o . }

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Workflow Biomart Protein Sequence Retrieval (1)

Created: 09/03/09 @ 11:38:10

Credits: User Kieren Lythgow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format.

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Workflow Using CQL to query protein sequence data (1)

Created: 07/05/09 @ 14:28:59

Credits: User Stian Soiland-Reyes

Attributions: Workflow Using CQL to query protein sequence data

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR Adapted from http://www.myexperiment.org/workflows/600

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Workflow Fetch PDB flatfile from RCSB server (1)

Created: 03/07/09 @ 14:37:14 | Last updated: 03/07/09 @ 14:53:40

Credits: User Stian Soiland-Reyes

Attributions: Workflow Fetch PDB flatfile from RCSB server Workflow Fetch PDB flatfile from RCSB server

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Workflow Tab Parser (1)

Created: 19/08/09 @ 16:05:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a tab separated file, and then parses specific rows and columns from the file into an Ondex Graph. Additional prarameters are provided, though these are optional: graphId Long the ID of the Graph (REQUIRED) input String the plugin input (REQUIRED) skip Integer How many rows to skip at begin of document (Optional). Default value is 22. fromCol Integer Index of concept parser id for from concept. Default value is 0. (REQUIRED) toCol Integer Index of concept par...

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Workflow Pfam Based Ortholog Filter (1)

Created: 19/08/09 @ 16:26:55

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters an Ondex graph based on the occurrence of Pfam orthologs within the graph. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ConfidenceThreshold - Threshold value for inparanoid confidence. Default value is 100. AnnotationScoreThreshold - Threshold...

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Workflow Sample Entity Converter (1)

Created: 08/09/09 @ 15:13:44 | Last updated: 14/09/09 @ 14:14:32

Credits: User Pedro Lopes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Disclaimer: This workflow is just a simple example designed for academic purposes.

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Workflow Parse unique proteins from Blast file (1)

Created: 19/03/10 @ 14:07:24 | Last updated: 19/03/10 @ 14:09:22

Credits: User Ian Laycock Network-member nclteamc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.

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Workflow retrieve protein sequence and do a BLAST a... (1)

Created: 21/07/10 @ 13:10:40 | Last updated: 21/07/10 @ 13:10:41

Credits: User Lebreton

Attributions: Workflow BLAST using DDBJ service

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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retrieve protein sequence and do a BLAST and extract position from DDBJ Web services   informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp  

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Workflow retrieve protein sequence and do a high sp... (1)

Created: 21/07/10 @ 13:16:00 | Last updated: 21/07/10 @ 13:23:12

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100

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Workflow retrieve protein sequence and do a BLAST w... (1)

Created: 21/07/10 @ 13:24:56 | Last updated: 01/09/10 @ 17:37:48

Credits: User Lebreton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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retrieve protein sequence and do a BLAST with options from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html exxample accession : Q9NRA8 database : UNIPROT program : blastp param : -b 5 -m 7    

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Workflow BLAST against the GPCRDB (1)

Created: 24/08/10 @ 13:45:14 | Last updated: 24/08/10 @ 13:45:16

Credits: User Bas Vroling

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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With this workflow you can submit a BLAST query to the GPCRDB. Input requires a sequence with amino acids only.

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Workflow Retrieve a protein from the GPCRDB (1)

Created: 24/08/10 @ 13:37:05 | Last updated: 24/08/10 @ 13:42:54

Credits: User Bas Vroling

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This small workflow illustrates how to use the web service access provided by the GPCRDB in Taverna. The proteinId input field is case sensitive and by default the identifiers in the GPCRDB are lowercase. You can try this mini-workflow with e.a. 'adrb2_human'.

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Workflow Create custom-made GPCR alignments (1)

Created: 24/08/10 @ 13:58:32 | Last updated: 24/08/10 @ 13:58:35

Credits: User Bas Vroling

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow allows you to create your own GPCR alignments. The alignments are built from the residues that are annotated with the general residue numbers. Alignments are therefore not built using standard alignment algorithms but are created by selecting residues that are likely to share the same position in the three-dimensional structure. Users can select the proteins and residue positions that should be aligned, allowing for the creation of e.g. an alignment of all binding pocket residue...

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Workflow M_Fetch_e-T_phylo_boot - (BETA) (1)

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

Credits: User Achille Zappa User Hamish McWilliam

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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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Workflow retrieve protein sequence and do a high sp... (1)

Created: 01/09/10 @ 17:16:24 | Last updated: 01/09/10 @ 17:18:45

Credits: User Lebreton

Attributions: Workflow retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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retrieve protein sequence and do a high speed BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100

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Workflow retrieve protein sequence and do a BLAST f... (1)

Created: 01/09/10 @ 17:22:14 | Last updated: 01/09/10 @ 17:22:37

Credits: User Lebreton

Attributions: Workflow retrieve protein sequence and do a BLAST and extract position from DDBJ Web services

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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retrieve protein sequence and do a BLAST from DDBJ Web services   informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp  

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Workflow InterProScan (SOAP) (1)

Created: 03/12/10 @ 07:41:47 | Last updated: 03/12/10 @ 07:41:48

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 Unported License

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Perform an InterProScan search using the EMBL-EBI’s InterProScan (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap). The query sequence to use is the input, the other parameters for the search are allowed to default.

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Workflow InterProScan (SOAP) (1)

Created: 03/12/10 @ 08:20:21 | Last updated: 03/12/10 @ 08:20:24

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow InterProScan (SOAP)

License: Creative Commons Attribution 3.0 Unported License

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Perform an InterProScan search using the EMBL-EBI’s InterProScan (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap). The query sequence to use is the input, the other parameters for the search are allowed to default.

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Workflow EMBL-EBI ClustalW2_SOAP (1)

Created: 17/01/11 @ 16:48:40 | Last updated: 17/01/11 @ 16:48:37

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EMBL-EBI ClustalW2 (SOAP) Workflow EBI_ClustalW2

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap). This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. Perform a ClustalW2 alignment using the EMBL-EBI’s C...

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Workflow Phylogenetic analysis workflow (1)

Created: 12/03/11 @ 07:10:59 | Last updated: 12/03/11 @ 07:12:22

Credits: User Yosr Bouhlal

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow provides a simple phylogenetic analysis starting from a protein query using "MrBayes" program and according to the maximum likelihood model

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Workflow Extract unique proteins from blast results (4)

Created: 24/03/11 @ 19:49:43 | Last updated: 01/04/11 @ 12:26:27

Credits: User Morgan Taschuk Network-member A Team

Attributions: Workflow Parse unique proteins from Blast file

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow parses uses the tab-delimited BLAST results to determine the unique proteins found in the target genome that have no similarity to the source genome.The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.This workflow allows you to configure a BioMart query to fetch sequ...

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Workflow Drug Re-Purposing Workflow (6)

Created: 25/03/11 @ 20:06:13 | Last updated: 01/04/11 @ 12:40:56

Credits: User Morgan Taschuk Network-member A Team

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screene...

Rating: 0.0 / 5 (0 ratings) | Versions: 6 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Threshold BLAST results (2)

Created: 28/03/11 @ 11:57:51 | Last updated: 01/04/11 @ 12:28:38

Credits: User Morgan Taschuk Network-member A Team

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Thresholds tab-delimited BLAST results to a certain percent identity.

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Workflow DAS sequence retrieval (2)

Created: 30/05/11 @ 01:20:35 | Last updated: 30/05/11 @ 01:26:47

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS).

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Workflow DAS sequence retrieval and parsing with JDAS (1)

Created: 30/05/11 @ 03:12:23 | Last updated: 30/05/11 @ 03:14:03

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS, copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.

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Workflow BLAST your sequences against the NucleaRDB (1)

Created: 19/08/11 @ 10:32:03 | Last updated: 19/08/11 @ 10:41:38

Credits: User Bas Vroling

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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BLAST your sequences against the NucleaRDB. Input requires a sequence with amino acids only (no fasta format etc)

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Workflow Simple protein distance phylogeny workflow (1)

Created: 22/09/11 @ 16:47:46 | Last updated: 22/09/11 @ 16:47:49

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Performs a multiple alignment and makes a phylogeny using a distance method on a set of protein sequences  

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Workflow Find Orthologs for proteins in Ensembl (1)

Created: 03/10/11 @ 14:33:04 | Last updated: 03/10/11 @ 14:33:07

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find Orthologs for proteins in Ensembl using biomart.

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Workflow KEIO Bioinformatics Web Service - a genera... (2)

Created: 13/08/10 @ 14:02:59 | Last updated: 19/11/10 @ 05:32:37

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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This workflow generates a sequence logo image for a set of amino acid sequences of FOXP2 gene, by downloading the amino acid sequences in Fasta format through Togo Web Service with UniProt identifiers (togoWS, provided by the G-language Genome Analysis Environment SOAP Service), running BLAST web service (runBLAST), retrieving a set of sequences from ID list (togoWS), aligning the sequence with MUSCLE (runMUSCLE), extracting a certain region from the alignment (extractalign, provided by Soapl...

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Workflow Find protein identifications in PRIDE (2)

Created: 21/02/12 @ 23:09:14 | Last updated: 22/02/12 @ 21:00:14

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find protein identifications information in the PRIDE database using a protein accession as input.

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Workflow Match gene lists based on information in l... (7)

Created: 17/04/12 @ 08:55:46 | Last updated: 25/04/12 @ 07:54:26

Credits: User Marco Roos User Reinout van Schouwen User Eleni User Kristina Hettne Network-member BioSemantics

Attributions: Workflow Match concept profiles Workflow Explain concept scores

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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[THIS WORKFLOW IS IN BETA STAGE] This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes. Example to explain (by analogy): When a group of informatic...

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Workflow NCBI Protein Clustal Omega Alignment (1)

Created: 31/08/12 @ 19:18:55

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Searches NCBI Proteins for a given organism and protein. User VMatch (xmknr) Vmatch, a versatile software tool for efficiently solving large scale sequence matching tasks to remove possible dubplcate and clustal omega to generate a multiple sequence alignment. Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make u...

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Creator

Pack BioExtract Server Workflow Tutorial


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

A tutorial to demonstrate how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.

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