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Items tagged with "FASTA" (21)

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Workflows (21)
Original Uploader

Workflow Protein_alignment_transmembrane (1)

Created: 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 Unported License

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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: 208 times | Downloaded: 59 times

Tags (16):

Original Uploader

Workflow EBI_FASTA (1)

Created: 30/05/08 @ 23:50:46 | Last updated: 06/12/10 @ 10:52:25

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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: 99 times | Downloaded: 50 times

Tags (6):

Original Uploader

Workflow EBI FASTA with prompts (3)

Created: 30/05/08 @ 23:53:16 | Last updated: 06/12/10 @ 10:53:23

Credits: User Hamish McWilliam

Attributions: Workflow EBI_FASTA

License: Creative Commons Attribution 3.0 Unported License

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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: 98 times | Downloaded: 47 times

Tags (7):

Original Uploader

Workflow Retrieve Protein Sequence and BLAST (1)

Created: 09/11/07 @ 10:41:12 | Last updated: 05/06/08 @ 15:18:07

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 315 times | Downloaded: 13 times

Tags (6):

Original Uploader

Workflow Biomart Protein Sequence Retrieval (1)

Created: 09/03/09 @ 11:38:10

Credits: User Kieren Lythgow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 200 times | Downloaded: 48 times

Tags (5):

Original Uploader

Workflow fetch_fasta (1)

Created: 20/03/09 @ 11:22:45 | Last updated: 20/03/09 @ 11:29:16

Credits: User Jumblejumble

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 173 times | Downloaded: 81 times

Tags (11):

Original Uploader

Workflow Example 3 (1)

Created: 20/10/09 @ 17:00:59

Credits: User Ruben

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Search in the Datenbank SWISS the Sequence 1220173

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Original Uploader

Workflow Ex (1)

Created: 16/11/09 @ 12:37:25

Credits: User Mventosa

Attributions: Workflow EBI_InterProScan for Taverna 2

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Ex of exercise

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 50 times | Downloaded: 0 times

Tags (3):

Original Uploader

Workflow Compare genome, extract proteins which are... (1)

Created: 19/03/10 @ 13:16:24 | Last updated: 19/03/10 @ 13:33:53

Credits: User Ian Laycock Network-member nclteamc

Attributions: Workflow fetchEnsemblSeqsAndBlast Workflow NCBI Gi to Kegg Pathways Workflow color_pathway_by_objects

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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  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: 176 times | Downloaded: 67 times

Tags (7):

Original Uploader

Workflow Retrieve Genome Seqn using gi nos (1)

Created: 19/03/10 @ 15:17:53

Credits: User Ian Laycock Network-member nclteamc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 29 times | Downloaded: 12 times

Tags (5):

Original Uploader

Workflow G-language Genome Analysis Environment - B... (2)

Created: 05/04/10 @ 06:08:25 | Last updated: 05/04/10 @ 06:08:26

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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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: 71 times | Downloaded: 46 times

Tags (5):

Original Uploader

Workflow Extract unique proteins from blast results (4)

Created: 24/03/11 @ 19:49:43 | Last updated: 01/04/11 @ 12:26:27

Credits: User Morgan Taschuk Network-member A Team

Attributions: Workflow Parse unique proteins from Blast file

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 61 times | Downloaded: 25 times

Tags (8):

Original Uploader

Workflow Drug Re-Purposing Workflow (6)

Created: 25/03/11 @ 20:06:13 | Last updated: 01/04/11 @ 12:40:56

Credits: User Morgan Taschuk Network-member A Team

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 75 times | Downloaded: 32 times

Tags (7):

Original Uploader

Workflow Compile Protein FASTA from Target to Drug ... (1)

Created: 30/03/11 @ 10:34:37 | Last updated: 30/03/11 @ 10:34:40

Credits: User Morgan Taschuk User Andrewsmeaton

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 14 times | Downloaded: 10 times

Tags (3):

Original Uploader

Workflow EBI NCBI BLAST Multi FASTA (2)

Created: 16/07/11 @ 19:08:38 | Last updated: 16/07/11 @ 19:35:11

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 44 times | Downloaded: 31 times

Tags (6):

Original Uploader

Workflow KEIO Bioinformatics Web Service - a genera... (2)

Created: 13/08/10 @ 14:02:59 | Last updated: 19/11/10 @ 05:32:37

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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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: 50 times | Downloaded: 34 times

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Original Uploader

Workflow Transform 'Stitch Gene blocks' FASTA block... (1)

Created: 16/07/12 @ 21:33:18 | Last updated: 16/07/12 @ 23:42:06

License: No license

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Converts FASTA blocks to a FASTA file. Workflow published by galaxyproject on Galaxy Jun 27, 2012 imported to myExperiment Jul16, 2012 during demonstration of Galaxy-myExperiment integration  https://main.g2.bx.psu.edu/u/galaxyproject/w/transform-stitch-gene-blocks-fasta-blocks-to-standardized-fasta-file

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 14 times | Downloaded: 1 time

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Original Uploader

Workflow de Bruin et al. Workflow 1 (1)

Created: 01/08/12 @ 08:50:28 | Last updated: 01/08/12 @ 08:54:59

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is "Workflow 1" from de Bruin et al., Mol. Cell. Proteomics 2012.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 31 times | Downloaded: 4 times

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Original Uploader

Workflow de Bruin et al. Workflow 2 (1)

Created: 01/08/12 @ 09:00:25 | Last updated: 01/08/12 @ 09:02:17

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is "Workflow 2" from de Bruin et al., Mol. Cell. Proteomics 2012.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 11 times | Downloaded: 7 times

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Original Uploader

Workflow de Bruin et al. Workflow 3 (1)

Created: 01/08/12 @ 09:03:01 | Last updated: 01/08/12 @ 09:07:18

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is "Workflow 3" from de Bruin et al., Mol. Cell. Proteomics 2012.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 15 times | Downloaded: 3 times

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Original Uploader

Workflow de Bruin et al. Workflow 4 (1)

Created: 01/08/12 @ 09:08:13 | Last updated: 01/08/12 @ 09:08:58

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is "Workflow 4" from de Bruin et al., Mol. Cell. Proteomics 2012.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 30 times | Downloaded: 3 times

Tags (6):

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