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Items tagged with "FASTA" (16)

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Workflows (16)

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: 185 times \| Downloaded: 52 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_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: 81 times \| Downloaded: 42 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: 83 times \| Downloaded: 41 times Tags (7): bioinformatics \| ebi \| FASTA \| sequence similarity search \| smith-waterman \| ssearch \| user_interaction	View Download (v3)
Taverna 1 Original Uploader Katy Wolstencroft	Retrieve Protein Sequence and BLAST (v1) Created: 09/11/07 @ 10:41:12 \| Last updated: 05/06/08 @ 15:18:07 Credits: Katy Wolstencroft License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieves a protein sequence in Fasta format from Genbank and then performs a BLAST on that sequence Rating: 4.0 / 5 (2 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 292 times \| Downloaded: 13 times Tags (6): BLAST \| ddbj \| FASTA \| genbank \| protein sequence \| searchsimple	View
Taverna 1 Original Uploader Kieren Lythgow	Biomart Protein Sequence Retrieval (v1) Created: 09/03/09 @ 11:38:10 Credits: Kieren Lythgow License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 174 times \| Downloaded: 44 times Tags (5): biomart \| ensembl \| FASTA \| protein \| sequence	View Download (v1)
Taverna 1 Original Uploader Jumblej...	fetch_fasta (v1) Created: 20/03/09 @ 11:22:45 \| Last updated: 20/03/09 @ 11:29:16 Credits: Jumblejumble License: Creative Commons Attribution-Share Alike 3.0 Unported License This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain. Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree. The output is prese... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 155 times \| Downloaded: 71 times Tags (11): alignment \| beanshell \| blastall \| database \| FASTA \| fetch \| file \| list \| strings \| text \| tree	View Download (v1)
Taverna 2 Original Uploader Ruben	Example 3 (v1) Created: 20/10/09 @ 17:00:59 Credits: Ruben License: Creative Commons Attribution-Share Alike 3.0 Unported License Search in the Datenbank SWISS the Sequence 1220173 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 73 times \| Downloaded: 26 times Tags (5): database \| FASTA \| in \| introduction \| taverna	View Download (v1)
Taverna 2 Original Uploader Mventosa	Ex (v1) Created: 16/11/09 @ 12:37:25 Credits: Mventosa Attributions: EBI_InterProScan for Taverna 2 License: Creative Commons Attribution-Share Alike 3.0 Unported License Ex of exercise Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 39 times \| Downloaded: 0 times Tags (3): FASTA \| tutorial exercise \| workflow	View
Taverna 2 Original Uploader Ian Laycock	Compare genome, extract proteins which are drug targets, apply to KEGG pathway (v1) Created: 19/03/10 @ 13:16:24 \| Last updated: 19/03/10 @ 13:33:53 Credits: Ian Laycock nclteamc Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects License: Creative Commons Attribution-Share Alike 3.0 Unported License Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga... Rating: 4.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 129 times \| Downloaded: 55 times Tags (7): colour \| FASTA \| gi \| kegg \| pathway \| proteins \| sequence	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	Retrieve Genome Seqn using gi nos (v1) Created: 19/03/10 @ 15:17:53 Credits: Ian Laycock nclteamc License: Creative Commons Attribution-Share Alike 3.0 Unported License Retrieves the genome seqn for both the target and source strains using gi nos Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 24 times \| Downloaded: 9 times Tags (5): FASTA \| genome \| gi \| nucleotide \| sequence	View Download (v1)
Taverna 2 Original Uploader cory (Kazuki Oshita)	G-language Genome Analysis Environment - Bacteria Analysis System (v2) Created: 05/04/10 @ 06:08:25 \| Last updated: 05/04/10 @ 06:08:26 Credits: cory (Kazuki Oshita) License: GNU General Public License (GPL) 2.0 Given an identifier for genome sequence (by default, genome of Mycoplasma genitalium: refseq:NC_000908) or raw sequence data in FASTA format, this workflow calculates and graphs the following properties using the G-language Genome Analysis Environment: GC skew (gcskew), cumulative GC skew (gcskew_cumulative), GC skew of coding/intergenic/GC3 (genomicskew), GC content with sliding windows (gcwin), replication origin and terminus (find_ori_ter), codon usage table (codon_usage), the Codon Adapta... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 53 times \| Downloaded: 33 times Tags (5): FASTA \| g-language \| genome \| sequence \| workflow	View Download (v2)
Taverna 2 Original Uploader Morgan Taschuk	Extract unique proteins from blast results (v4) Created: 24/03/11 @ 19:49:43 \| Last updated: 01/04/11 @ 12:26:27 Credits: Morgan Taschuk A Team Attributions: Parse unique proteins from Blast file License: Creative Commons Attribution-Share Alike 3.0 Unported License The workflow parses uses the tab-delimited BLAST results to determine the unique proteins found in the target genome that have no similarity to the source genome.The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.This workflow allows you to configure a BioMart query to fetch sequ... Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 17 times Tags (8): BLAST \| FASTA \| protein \| proteins \| proteome \| similarity \| tab \| uniqueness	View Download (v4)
Taverna 2 Original Uploader Morgan Taschuk	Drug Re-Purposing Workflow (v6) Created: 25/03/11 @ 20:06:13 \| Last updated: 01/04/11 @ 12:40:56 Credits: Morgan Taschuk A Team License: Creative Commons Attribution-Share Alike 3.0 Unported License The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screene... Rating: 0.0 / 5 (0 ratings) \| Versions: 6 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 38 times \| Downloaded: 25 times Tags (7): BLAST \| FASTA \| protein \| proteins \| proteome \| similarity \| uniqueness	View Download (v6)
Taverna 2 Original Uploader Morgan Taschuk	Compile Protein FASTA from Target to Drug file (v1) Created: 30/03/11 @ 10:34:37 \| Last updated: 30/03/11 @ 10:34:40 Credits: Morgan Taschuk Andrewsmeaton License: Creative Commons Attribution-Share Alike 3.0 Unported License Uses a tab-delimited file with protein target and drug information (created in Ondex) to compile a protein FASTA file including each target. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 8 times \| Downloaded: 7 times Tags (3): FASTA \| tab-delimited \| uniprot	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	EBI NCBI BLAST Multi FASTA (v2) Created: 16/07/11 @ 19:08:38 \| Last updated: 16/07/11 @ 19:35:11 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs multiple sequence similarity searches using the NCBI blast at the EBI. It uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. If you want to make a blast search for more than 10 sequences I would recommend you to run the workflow using the comm... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 9 times Tags (6): BLAST \| ebi \| FASTA \| fasta format \| sequence \| similarity	View Download (v2)
Taverna 2 Original Uploader cory (Kazuki Oshita)	KEIO Bioinformatics Web Service - a generating sequence logo image for a set of sequence retrieval via homology search (v2) Created: 13/08/10 @ 14:02:59 \| Last updated: 19/11/10 @ 05:32:37 Credits: cory (Kazuki Oshita) License: GNU General Public License (GPL) 2.0 This workflow generates a sequence logo image for a set of amino acid sequences of FOXP2 gene, by downloading the amino acid sequences in Fasta format through Togo Web Service with UniProt identifiers (togoWS, provided by the G-language Genome Analysis Environment SOAP Service), running BLAST web service (runBLAST), retrieving a set of sequences from ID list (togoWS), aligning the sequence with MUSCLE (runMUSCLE), extracting a certain region from the alignment (extractalign, provided by Soapl... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 26 times Tags (9): BLAST \| FASTA \| g-language \| kbws \| muscle \| protein \| sequence \| togows \| weblogo	View Download (v2)