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EB-eye getAllResultIds and WSDbfetch fetch...
(1)
Get database entries for a query using EB-eye to perform the initial query against the database to get entry identifiers and using the identifiers with WSDbfetch to retrieve the entry data in the desired format.
Note: this particular implementation is not suitable for queries which return large numbers of results.
Created: 2013-03-28
Credits:
Hamish McWilliam
EMBL-EBI ClustalW2 (SOAP)
(1)
Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).
Created: 2010-12-06
| Last updated: 2013-03-28
Attributions:
EBI_ClustalW2
InterProScan (SOAP)
(1)
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.
Created: 2010-12-03
| Last updated: 2013-03-28
Credits:
Hamish McWilliam
Attributions:
EBI_InterProScan
InterProScan (SOAP)
InterProScan (SOAP)
(1)
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.
Created: 2010-12-03
| Last updated: 2013-03-28
Attributions:
EBI_InterProScan
NCBI BLAST (SOAP)
(1)
Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.
Created: 2010-11-29
| Last updated: 2013-03-28
Credits:
Hamish McWilliam
Attributions:
EBI_NCBI_BLAST
NCBI BLAST (SOAP)
NCBI BLAST (SOAP)
(1)
Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.
Created: 2010-11-29
| Last updated: 2013-03-28
Attributions:
EBI_NCBI_BLAST
NCBI BLAST (SOAP)
EBI WU-BLAST with program and database sel...
(3)
Run a BLAST analysis using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). 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:
Hamish McWilliam
Attributions:
EBI_WU-BLAST
Protein_search_fetch_align_tree
(2)
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...
Created: 2009-04-07
Credits:
Hamish McWilliam
Attributions:
EBI_ClustalW2
EBI_ClustalW2_phylogentic_tree
EBI_dbfetch_fetchBatch
EBI_WU-BLAST
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 http://www.ebi.ac.uk/Tools/webservices/services/clustalw2).
Created: 2009-04-07
Credits:
Hamish McWilliam
EBI_ClustalW2
(2)
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.
Note: the WSClustalW2 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 ClustalW2 servi...
Created: 2009-04-07
| Last updated: 2010-12-06
Credits:
Hamish McWilliam
Protein_transmembrane_prediction
(2)
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...
Created: 2008-10-26
| Last updated: 2011-04-01
Credits:
Hamish McWilliam
Attributions:
EBI_InterProScan_tmhmm_signalp
EBI_Phobius
tmap_single_sequence
Nucleotide_InterProScan
(4)
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...
Created: 2008-10-26
| Last updated: 2011-04-01
Credits:
Hamish McWilliam
Attributions:
EBI_InterProScan
EBI_NCBI_BLAST
Nucleotide_ORF_translation
Fasta_string_to_fasta_list
Sequence_or_ID
EBI_InterProScan_tmhmm_signalp
(4)
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...
Created: 2008-10-26
| Last updated: 2011-04-01
Credits:
Hamish McWilliam
Attributions:
EBI_InterProScan
EBI_Blast2InterPro
(2)
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...
Created: 2008-10-26
| Last updated: 2012-08-22
Credits:
Hamish McWilliam
Attributions:
EBI_WU-BLAST
EBI_dbfetch_fetchBatch
Fasta_string_to_fasta_list
EBI_InterProScan
EBI_InterProScan
(3)
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 an InterProScan ...
Created: 2008-10-26
| Last updated: 2011-04-01
Credits:
Hamish McWilliam
EBI_IntAct
(1)
Find protein binary interactions using the EBI's IntAct service.
See http://www.ebi.ac.uk/intact/ for further details.
Created: 2008-07-09
Credits:
Hamish McWilliam
EBI_OLS_TermInfo
(1)
Get details of an ontology term given its identifer.
This workflow uses the EBI's Ontology Lookup Service (OLS) to get the details of the ontology term. The OLS suports a wide range of biological and bioinformatic ontologies. See http://www.ebi.ac.uk/ontology-lookup/ for more information.
Created: 2008-07-09
Credits:
Hamish McWilliam
EBI_Whatizit
(1)
Perform a text-mining analysis of an input text document using the EBI's Whatizit tool (http://www.ebi.ac.uk/webservices/whatizit/info.jsf).
Whatizit provides a number of text-mining pipelines which can can detect various terms of biological interest in text documents. For example finding gene names and mapping them to UniProtKB identifiers, finding chemical terms and mapping them to ChEBI, etc.
Created: 2008-07-09
Credits:
Hamish McWilliam
EBI_CiteXplore
(1)
Perform a literature search using the EBI's CiteXplore service (http://www.ebi.ac.uk/citexplore/), and get the results in a minimal XML format containing the citation information (i.e. title, author, journal, etc.), the identifier of the citation in the source database (PubMed/Medline, Agricola, Patent Abstracts, CBA, CiteSeer, etc.) and information about abstract and full article availablity including URLs.
Created: 2008-07-09
Credits:
Hamish McWilliam
tRNAscan
(1)
Search a nucleotide sequence for tRNA genes using the tRNAscan-SE tool (see http://wiki.bioinformatics.org/TRNAscan-SE).
This workflow uses the tRNAscan service at VBI PathPort (see http://pathport.vbi.vt.edu/services/#predict_7).
Created: 2008-06-28
Credits:
Hamish McWilliam
Attributions:
Sequence_or_ID_or_GI
EBI_CENSOR
(2)
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.
Created: 2008-06-17
| Last updated: 2008-06-25
Credits:
Hamish McWilliam
EBI_Fetch_InterPro_Matches_UniParc
(1)
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).
Created: 2008-06-08
Credits:
Hamish McWilliam
EBI_dbfetch_UniParc
(1)
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).
Created: 2008-06-08
Credits:
Hamish McWilliam
EBI_PICR_Sequence_to_ID
(1)
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.
Created: 2008-06-08
Credits:
Hamish McWilliam
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 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...
Created: 2008-06-08
| Last updated: 2008-06-08
Credits:
Hamish McWilliam
Attributions:
EBI_dbfetch_UniParc
EBI_Fetch_InterPro_Matches_UniParc
EBI_PICR_Sequence_to_ID
EBI_DaliLite
(1)
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.
Created: 2008-06-07
Credits:
Hamish McWilliam
Sequence_or_ID_or_GI
(1)
Get a sequence in fasta format given one of:
An NCBI GI number (e.g. 75251068).
An entry identifier in database:identifier format (e.g. uniprot:Q96247).
3. A sequence entry in a format supported by EMBOSS seqret.
Created: 2008-06-07
Credits:
Hamish McWilliam
Attributions:
Structure_or_ID
NCBI_QBLAST
(2)
Perform an NCBI BLAST sequence similarity search using NCBI's QBLAST service (see http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.
Created: 2008-06-07
| Last updated: 2008-06-07
Credits:
Hamish McWilliam
Nucleotide_ORF_translation
(1)
From a nucleotide sequence get the protein translations of the open reading frames (stop to stop) that are longer than a specifed minimum length.
EMBOSS getorf is used to find the ORFs and perform the translations. The getorf tool is accessed via Soaplab (see http://www.ebi.ac.uk/Tools/webservices/soaplab/overview).
Created: 2008-06-06
Credits:
Hamish McWilliam
Attributions:
Sequence_or_ID
Structure_or_ID
(1)
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.
Created: 2008-06-06
Credits:
Hamish McWilliam
EBI_MaxSprout
(2)
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.
Created: 2008-06-05
| Last updated: 2008-06-06
Credits:
Hamish McWilliam
Attributions:
Structure_or_ID
EBI_TCoffee
(1)
Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSTCoffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) is used.
Note: the WSTCoffee 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 T-COFFEE services (REST or SOAP) should be used instead.
Created: 2008-06-03
| Last updated: 2010-12-06
Credits:
Hamish McWilliam
EBI_MUSCLE
(1)
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.
Note: the WSMuscle 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 MUSCLE services (REST or SOAP) should be used instead.
Created: 2008-06-03
| Last updated: 2010-12-06
Credits:
Hamish McWilliam
EBI_ScanPS
(1)
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.
Created: 2008-06-03
| Last updated: 2010-12-06
Credits:
Hamish McWilliam
EBI_MAFFT
(1)
Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool.
Note: the WSMafft 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 MAFFT services (REST or SOAP) should be used instead.
Created: 2008-06-03
| Last updated: 2010-12-06
Credits:
Hamish McWilliam
EBI_MPsrch
(1)
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.
Created: 2008-06-02
| Last updated: 2010-12-06
Credits:
Hamish McWilliam
EBI_Kalign
(1)
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.
Note: the WSKalign service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. Thi...
Created: 2008-06-02
| Last updated: 2010-12-06
Credits:
Hamish McWilliam
Sequence_or_ID
(1)
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)
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_Phobius
(2)
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.
Created: 2008-06-01
| Last updated: 2008-06-02
Credits:
Hamish McWilliam
EBI_dbfetch_fetchBatch
(1)
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_blastpgp_PSI-BLAST
(1)
Perform a PSI-BLAST iterative search using the EBI’s WSBlastpgp service (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp). The query sequence, database to search and users e-mail address are inputs, the other parameters for the search (see Job_params) are allowed to default. In most cases you will probably want to adjust the expectation thresholds and the maximum number of iterations for your specific query sequence and the database being searched.
Created: 2008-05-31
Credits:
Hamish McWilliam
EBI_ClustalW_alignment_tree
(2)
Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks.
Created: 2008-05-31
| Last updated: 2010-12-03
Credits:
Hamish McWilliam
Attributions:
EBI_ClustalW2
EBI_ClustalW2_phylogentic_tree
EBI_InterProScan_with_prompts
(1)
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 an InterProScan anal...
Created: 2008-05-31
| Last updated: 2011-04-01
Credits:
Hamish McWilliam
Attributions:
EBI_InterProScan
EBI_NCBI_BLAST_with_prompts
(1)
Run a BLAST analysis using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). This workflow wraps the EBI_NCBI_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.
Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be use...
Created: 2008-05-31
| Last updated: 2010-12-06
Credits:
Hamish McWilliam
Attributions:
EBI_NCBI_BLAST
EBI_NCBI_BLAST
(1)
Perform a BLAST search using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). 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:
Hamish McWilliam
EBI FASTA with prompts
(3)
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
EBI_FASTA
(1)
Run a FASTA or SSEARCH sequence similarity search using the EBI's WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta).
Note: the WSFasta 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 FASTA services (REST or SOAP) should be used instead.
Created: 2008-05-30
| Last updated: 2010-12-06
Credits:
Hamish McWilliam
EBI_WU-BLAST
(1)
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