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Items tagged with "sequence similarity search" (15)

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Workflows (15)

Taverna 1 Original Uploader Hamish McWilliam	EBI_WU-BLAST (v1) Created: 30/05/08 @ 22:47:18 \| Last updated: 06/12/10 @ 10:51:04 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 209 times \| Downloaded: 78 times Tags (5): bioinformatics \| BLAST \| ebi \| sequence similarity search \| wu-blast	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI WU-BLAST with program and database selection prompts. (v3) Created: 04/07/09 @ 11:39:54 \| Last updated: 06/12/10 @ 10:56:44 Credits: Hamish McWilliam Attributions: EBI_WU-BLAST License: Creative Commons Attribution 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 169 times \| Downloaded: 82 times Tags (6): bioinformatics \| BLAST \| ebi \| sequence similarity search \| user_interaction \| wu-blast	View Download (v3)
Taverna 1 Original Uploader Hamish McWilliam	EBI_FASTA (v1) Created: 30/05/08 @ 23:50:46 \| Last updated: 06/12/10 @ 10:52:25 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 85 times \| Downloaded: 49 times Tags (6): bioinformatics \| ebi \| FASTA \| sequence similarity search \| smith-waterman \| ssearch	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI FASTA with prompts (v3) Created: 30/05/08 @ 23:53:16 \| Last updated: 06/12/10 @ 10:53:23 Credits: Hamish McWilliam Attributions: EBI_FASTA License: Creative Commons Attribution 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 86 times \| Downloaded: 44 times Tags (7): bioinformatics \| ebi \| FASTA \| sequence similarity search \| smith-waterman \| ssearch \| user_interaction	View Download (v3)
Taverna 1 Original Uploader Hamish McWilliam	EBI_NCBI_BLAST (v1) Created: 31/05/08 @ 08:38:46 \| Last updated: 06/12/10 @ 10:54:16 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 312 times \| Downloaded: 154 times Tags (6): bioinformatics \| BLAST \| blastall \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_NCBI_BLAST_with_prompts (v1) Created: 31/05/08 @ 08:40:29 \| Last updated: 06/12/10 @ 10:55:09 Credits: Hamish McWilliam Attributions: EBI_NCBI_BLAST License: Creative Commons Attribution 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 109 times \| Downloaded: 73 times Tags (7): bioinformatics \| BLAST \| blastall \| ebi \| ncbi blast \| sequence similarity search \| user_interaction	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_blastpgp_PSI-BLAST (v1) Created: 31/05/08 @ 14:39:22 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 123 times \| Downloaded: 61 times Tags (7): bioinformatics \| BLAST \| blastpgp \| ebi \| ncbi blast \| PSI-BLAST \| sequence similarity search	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Protein_search_fetch_align_tree (v2) Created: 07/04/09 @ 20:13:19 Credits: Hamish McWilliam Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST License: Creative Commons Attribution 3.0 Unported License An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 419 times \| Downloaded: 140 times Tags (15): alignment \| bioinformatics \| BLAST \| clustal \| clustalw \| dbfetch \| ebi \| multiple sequence alignment \| neighbor-joining \| phylogenetic tree \| protein \| sequence alignment \| sequence similarity search \| tree \| wu-blast	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Protein_alignment_transmembrane (v1) Created: 01/06/08 @ 12:20:29 Credits: Hamish McWilliam Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch License: Creative Commons Attribution 3.0 Unported License 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: 190 times \| Downloaded: 57 times Tags (16): alignment \| bioinformatics \| clustal \| clustalw \| dbfetch \| ebi \| emboss \| emboss tmap \| FASTA \| multiple sequence alignment \| protein \| protein annotation \| sequence alignment \| sequence similarity search \| transmembrane \| transmembrane prediction	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_MPsrch (v1) Created: 02/06/08 @ 21:49:11 \| Last updated: 06/12/10 @ 10:38:42 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 64 times \| Downloaded: 43 times Tags (7): bioinformatics \| ebi \| mpsrch \| protein \| protein annotation \| sequence similarity search \| smith-waterman	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ScanPS (v1) Created: 03/06/08 @ 05:57:09 \| Last updated: 06/12/10 @ 10:37:50 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 58 times \| Downloaded: 38 times Tags (6): bioinformatics \| ebi \| protein \| scanps \| sequence similarity search \| smith-waterman	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_Blast2InterPro (v2) Created: 26/10/08 @ 20:45:45 \| Last updated: 01/04/11 @ 08:55:49 Credits: Hamish McWilliam Attributions: EBI_WU-BLAST EBI_dbfetch_fetchBatch Fasta_string_to_fasta_list EBI_InterProScan License: Creative Commons Attribution 3.0 Unported License 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: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 245 times \| Downloaded: 94 times Tags (11): bioinformatics \| BLAST \| dbfetch \| ebi \| go terms \| interpro \| interproscan \| protein \| protein annotation \| sequence similarity search \| wu-blast	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	NCBI_QBLAST (v2) Created: 07/06/08 @ 15:05:00 \| Last updated: 07/06/08 @ 17:11:36 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 136 times \| Downloaded: 70 times Tags (5): bioinformatics \| BLAST \| ncbi \| ncbi blast \| sequence similarity search	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	NCBI BLAST (SOAP) (v1) Created: 29/11/10 @ 20:46:58 \| Last updated: 29/11/10 @ 20:47:00 Credits: Hamish McWilliam Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP) License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 29 times \| Downloaded: 16 times Tags (7): bioinformatics \| BLAST \| blastall \| blastp \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)
Taverna 2 Original Uploader Hamish McWilliam	NCBI BLAST (SOAP) (v1) Created: 29/11/10 @ 20:03:13 \| Last updated: 29/11/10 @ 20:03:14 Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP) License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 44 times \| Downloaded: 61 times Tags (7): bioinformatics \| BLAST \| blastall \| blastp \| ebi \| ncbi blast \| sequence similarity search	View Download (v1)