Workflows

tmap_single_sequence (2)

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

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

Credits: Hamish McWilliam

Attributions: Sequence_or_ID

Sequence_or_ID (1)

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Given a sequence or sequence entry identifer (e.g. uniprot:wap_rat), return the sequence in fasta format. If a sequence 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 sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format.

Created: 2008-06-01

Credits: Hamish McWilliam

Protein_alignment_transmembrane (1)

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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...

Created: 2008-06-01

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch

EBI_WU-BLAST (1)

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Perform a BLAST search using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). The default parameters search UniProtKB using blastp. To change the job parameters see Job_params. Note: the WSWUBlast 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 WU-BLAST services (REST or SOAP) should be used instead.  

Created: 2008-05-30 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Identification of differential genes using... (2)

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This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data for analysis using t-tests by R. A list of significant differentially expressed genes is then analysed using the Go Term Finder tool which generates a list of GO terms associated with the genes. A CSV file containing the list of significant genes is also generated.

Created: 2008-04-15 | Last updated: 2008-07-01

Credits: Peter Li

GBSeq test (2)

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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.

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

Credits: Franck Tanoh

EBI NCBI Blast (2)

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EBI NCBI Blast

Created: 2007-10-03

Nucleotide InterProScan for the BioExtract... (3)

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This workflow can be downloaded and imported into the BioExtract Server at bioextract.org. This workflow is a BioExtract Server process similar to the Nucleotide InterProScan workflow designed and implement in Taverna by Hamish McWilliams. The InterProScan tool (http://www.ebi.ac.uk/Tools/InterProScan/) 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: Carol Lushbough Hamish McWilliam

Attributions: Nucleotide_InterProScan

EBI_dbfetch_fetchBatch (1)

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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).

Created: 2008-05-31

Credits: Hamish McWilliam

EBI FASTA with prompts (3)

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Run a FASTA analysis using the EBI’s WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). This workflow wraps the EBI_FASTA workflow to provide a basic user interface which prompts for the required inputs: sequence, database, FASTA program and user e-mail. Other parameters (e.g. matrix, gap penalties, etc.) are allowed to default. Note: the WSFasta service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new developme...

Created: 2008-05-30 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Attributions: EBI_FASTA