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Pack EBI Web Services

Created: 11/07/08 @ 01:24:33 | Updated: 11/07/08 @ 01:24:33

The European Bioinformatics Institiute offers a wide range of services covering may biological anfd bioinformatics domains. This Pack col.lates a set of workflows that provide wrappers for web services developed, and maintained by the EBI.

19 items in this pack

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Workflows (42)

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Workflow EBI_WU-BLAST (v1)

Created: 30/05/08 @ 22:47:18 | Updated: 02/06/08 @ 21:30:17

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_wu-blast_31786_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.

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Workflow EBI WU-BLAST with prompt (v2)

Created: 30/05/08 @ 22:56:49 | Updated: 02/06/08 @ 21:30:43

Credits: User Hamish McWilliam

Attributions: Workflow EBI_WU-BLAST

License: Creative Commons Attribution 3.0 License

Ebi_wu-blast_with_prompt_31025_2
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.

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Workflow EBI_FASTA (v1)

Created: 30/05/08 @ 23:50:46 | Updated: 02/06/08 @ 21:31:18

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_fasta_20674_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).

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Workflow EBI FASTA with prompts (v3)

Created: 30/05/08 @ 23:53:16 | Updated: 02/06/08 @ 21:31:41

Credits: User Hamish McWilliam

Attributions: Workflow EBI_FASTA

License: Creative Commons Attribution 3.0 License

Ebi_fasta_with_prompts_25201_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.

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Workflow EBI_NCBI_BLAST (v1)

Created: 31/05/08 @ 08:38:46 | Updated: 02/06/08 @ 21:32:21

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_ncbi_blast_8105_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.

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Workflow EBI_NCBI_BLAST_with_prompts (v1)

Created: 31/05/08 @ 08:40:29 | Updated: 02/06/08 @ 21:32:48

Credits: User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

License: Creative Commons Attribution 3.0 License

Ebi_ncbi_blast_with_prompts_25022_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.

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Workflow EBI_ClustalW2 (v1)

Created: 31/05/08 @ 10:27:58 | Updated: 02/06/08 @ 21:27:39

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_clustalw2_20041_1
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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Workflow EBI_InterProScan (v2)

Created: 31/05/08 @ 11:38:57 | Updated: 25/06/08 @ 06:30:59

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_interproscan_16782_2
Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...

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Workflow EBI_InterProScan_with_prompts (v1)

Created: 31/05/08 @ 11:40:34 | Updated: 31/05/08 @ 11:40:34

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 License

Ebi_interproscan_with_prompts_27955_1
Run an InterProScan analysis using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). This workflow wraps the EBI_InterProScan workflow to provide a basic user interface which prompts for the required inputs: protien sequence and user e-mail. Other parameters are allowed to default.

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Workflow EBI_ClustalW2_phylogentic_tree (v1)

Created: 31/05/08 @ 13:07:34 | Updated: 31/05/08 @ 13:07:34

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_clustalw2_phylogentic_tree_28905_1
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).

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Workflow EBI_ClustalW_alignment_tree (v1)

Created: 31/05/08 @ 13:53:04 | Updated: 31/05/08 @ 13:53:04

Credits: User Hamish McWilliam

Attributions: Workflow EBI_ClustalW2 Workflow EBI_ClustalW2_phylogentic_tree

License: Creative Commons Attribution 3.0 License

Ebi_clustalw_alignment_tree_19203_1
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.

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Workflow EBI_blastpgp_PSI-BLAST (v1)

Created: 31/05/08 @ 14:39:22 | Updated: 31/05/08 @ 14:39:22

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_blastpgp_psi-blast_11519_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.

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Workflow EBI_dbfetch_fetchBatch (v1)

Created: 31/05/08 @ 20:59:46 | Updated: 31/05/08 @ 20:59:46

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_dbfetch_fetchbatch_30338_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).

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Workflow Protein_search_fetch_align_tree (v1)

Created: 31/05/08 @ 21:09:15 | Updated: 31/05/08 @ 21:09:15

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 License

Protein_search_fetch_align_tree_3947_1
An implmentation of the classical sequence analysis workflow: 1. Find homologues (sequence similarity search) 2. Fetch homologues 3. Align homologues (multiple sequence alignment) 4. Produce phylogenetic tree In this implementation the EBI webservices are used: 1. WU-BLAST (WSWUBlast) blastp vs. UniProtKB 2. dbfetch (WSDbfetch) 3. ClustalW (WSClustalW2) 4. ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with ...

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Workflow EBI_Phobius (v2)

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

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_phobius_21230_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.

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Workflow EBI_InterProScan_tmhmm_signalp (v3)

Created: 01/06/08 @ 11:21:45 | Updated: 01/06/08 @ 15:05:36

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan

License: Creative Commons Attribution 3.0 License

Ebi_interproscan_tmhmm_signalp_9530_3
Use the TMHMM and SignalP methods of InterProScan to perform transmembrane and signal peptide prediction. The EBI's InterProScan web service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan) is used.

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Workflow Protein_alignment_transmembrane (v1)

Created: 01/06/08 @ 12:20:29 | Updated: 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 License

Protein_alignment_transmembrane_5019_1
Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: 1. Sequence similarity search (SSS) to find homologues 2. Fetch sequences of hits 3. Multiple sequence alignment (MSA) of hit sequences 4. EMBOSS tmap with alignment from 3. Uses the EBI web services: 1. WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) 2. WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) 3. WSClustalW2 (see http://www.ebi.ac.uk/Tools/webs...

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Workflow Sequence_or_ID (v1)

Created: 01/06/08 @ 14:15:12 | Updated: 01/06/08 @ 14:15:12

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Sequence_or_id_19146_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.

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Workflow tmap_single_sequence (v2)

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

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID

License: Creative Commons Attribution 3.0 License

Tmap_single_sequence_30612_2
Simple workflow using tmap to find transmembrane regions, using a single sequence as input.

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Workflow Protein_transmembrane_prediction (v1)

Created: 01/06/08 @ 17:49:30 | Updated: 01/06/08 @ 17:49:30

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan_tmhmm_signalp Workflow EBI_Phobius Workflow tmap_single_sequence

License: Creative Commons Attribution 3.0 License

Protein_transmembrane_prediction_5053_1
Transmembrane and signal peptide prediction using three methods: 1. EMBOSS tmap with a single sequence. Uses Soaplab tmap. 2. Phobius. Uses EBI's WSPhobius web service. 3. TMHMM and SignalP. Uses the TMHMM and SignalP methods of InterProScan via the EBI's WSInterProScan service. The results of the three methods are converted into GFF format and collated.

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Workflow EBI_Kalign (v1)

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

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_kalign_29379_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.

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Workflow EBI_MPsrch (v1)

Created: 02/06/08 @ 21:49:11 | Updated: 02/06/08 @ 21:49:11

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_mpsrch_820_1
Run a Smith-Waterman sequence search using the EBI’s WSMPsrch service (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch).

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Workflow EBI_MAFFT (v1)

Created: 03/06/08 @ 05:55:43 | Updated: 03/06/08 @ 05:55:43

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Ebi_mafft_21930_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.

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