Tag Results

Items tagged with "dbfetch" (11)

Note: some items may not be visible to you, due to viewing permissions.

Workflows (11)

Taverna 1 Original Uploader Hamish McWilliam	EBI_dbfetch_fetchBatch (v1) Created: 31/05/08 @ 20:59:46 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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). Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 103 times \| Downloaded: 70 times Tags (3): bioinformatics \| dbfetch \| ebi	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	Sequence_or_ID (v1) Created: 01/06/08 @ 14:15:12 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 144 times \| Downloaded: 60 times Tags (6): bioinformatics \| dbfetch \| ebi \| emboss \| emboss seqret \| sequence retrieval	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	Structure_or_ID (v1) Created: 06/06/08 @ 05:57:31 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 379 times \| Downloaded: 37 times Tags (8): bioinformatics \| dbfetch \| ebi \| pdb \| protein \| protein structure \| structure \| structure retrieval	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	Sequence_or_ID_or_GI (v1) Created: 07/06/08 @ 16:58:14 Credits: Hamish McWilliam Attributions: Structure_or_ID License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 118 times \| Downloaded: 60 times Tags (9): bioinformatics \| dbfetch \| ebi \| efetch \| fasta format \| gi \| ncbi \| sequence identifier \| sequence retrieval	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_PICR_Sequence_to_UniParc_and_InterPro (v2) Created: 08/06/08 @ 13:53:39 \| Last updated: 08/06/08 @ 14:10:02 Credits: Hamish McWilliam Attributions: EBI_dbfetch_UniParc EBI_Fetch_InterPro_Matches_UniParc EBI_PICR_Sequence_to_ID License: Creative Commons Attribution 3.0 Unported License 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: 158 times \| Downloaded: 57 times Tags (13): bioinformatics \| dbfetch \| ebi \| fasta format \| gi \| interpro \| picr \| protein \| sequence identifier \| sequence retrieval \| uniparc \| uniprot archive \| upi	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_dbfetch_UniParc (v1) Created: 08/06/08 @ 14:05:40 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 53 times \| Downloaded: 33 times Tags (9): bioinformatics \| dbfetch \| ebi \| protein \| sequence identifier \| sequence retrieval \| uniparc \| uniprot archive \| upi	View Download (v1)
Triana Original Uploader Hamish McWilliam	EBI_dbfetch_fetchData (v1) Created: 28/08/09 @ 11:45:50 \| Last updated: 28/08/09 @ 11:49:08 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Sample workflow illustrating the use of the EBI's WSDbfetch service in Triana. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 54 times \| Downloaded: 29 times Tags (4): bioinformatics \| dbfetch \| ebi \| sequence retrieval	View Download (v1)
Triana Original Uploader Hamish McWilliam	EBI_dbfetch_fetchBatch (v1) Created: 28/08/09 @ 11:55:10 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Sample workflow illustrating the use of EBI's WSDbfetch service with Triana. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 59 times \| Downloaded: 18 times Tags (5): bioinformatics \| dbfetch \| ebi \| example \| structure retrieval	View Download (v1)