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Items tagged with "proteins" (9)

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Workflows (9)

Taverna 2 Original Uploader Pedro Lopes	Get Bioentity from Organism (v1) Created: 08/09/09 @ 15:12:57 \| Last updated: 14/09/09 @ 14:16:40 Credits: Pedro Lopes License: Creative Commons Attribution-Share Alike 3.0 Unported License GeNS workflow that lists the identifiers corresponding to a given species and data type. For instance, list all OMIM associated with the human species. Disclaimer: This workflow is just a simple example designed for academic purposes. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 58 times \| Downloaded: 13 times Tags (5): genomic name server \| genomics \| gens \| proteins \| proteomics	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	Extract proteins using a gi - output as fasta file (v1) Created: 19/03/10 @ 13:54:54 Credits: Ian Laycock nclteamc License: Creative Commons Attribution-Share Alike 3.0 Unported License The workflow uses the gi id to retrieve a xml format of the genbank entry. Using a beanscript, the workflow then parses the required data for the creation of the protein fasta file. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 28 times \| Downloaded: 17 times Tags (2): gi \| proteins	View Download (v1)
Taverna 2 Original Uploader Ian Laycock	blastp of target vs source database (v1) Created: 19/03/10 @ 13:57:32 \| Last updated: 19/03/10 @ 14:05:40 Credits: Ian Laycock nclteamc Attributions: fetchEnsemblSeqsAndBlast License: Creative Commons Attribution-Share Alike 3.0 Unported License This worlflow allows the user to input two sets of proteins in fasta format. One file is converted to a database using formatdb, the set is blasted against this database to test for Blast hits. Users is able to set eValue and destination of files for database and blast file. Arguments can be added to either formatdb or blast in beanshell supplied. Blast and formatdb must be installed locally and the correct filepaths for these applications must entered into the workflow accordingly. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 13 times Tags (4): blastall \| blastp \| database \| proteins	View Download (v1)
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 Marco Roos	BioAID_ProteinDiscovery (v7) Created: 10/05/10 @ 16:21:09 \| Last updated: 12/01/12 @ 14:39:37 Credits: Marco Roos AID License: Creative Commons Attribution-Share Alike 3.0 Unported License The workflow extracts protein names from documents retrieved from MedLine based on a user Query (cf Apache Lucene syntax). The protein names are filtered by checking if there exists a valid UniProt ID for the given protein name. Rating: 0.0 / 5 (0 ratings) \| Versions: 7 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 258 times \| Downloaded: 116 times Tags (12): AIDA \| BioAID \| biorange_nl \| lucene \| protein \| proteins \| pubmed \| search \| text_mining \| text_mining_network \| uniprot \| VL-e	View Download (v7)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Open PDB entries in Jmol for hits found for HIV in Bio2RDF (v3) Created: 14/03/10 @ 21:26:05 \| Last updated: 23/06/10 @ 20:20:41 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Queries Bio2RDF for proteins of which the title contains 'HIV', downloads them using the EMBL webservices and opens them in Bioclipse for visualization with Jmol. Rating: 1.0 / 5 (2 ratings) \| Versions: 3 \| Reviews: 1 \| Comments: 0 \| Citations: 0 Viewed: 110 times \| Downloaded: 25 times Tags (10): bio2rdf \| bioclipse \| cheminformatics \| drug development \| hiv \| jmol \| pdb \| proteins \| rdf \| sparql	View Download (v3)
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)
BioExtract Server Original Uploader Carol Lushbough	tblastx non-redundant alignment (v1) Created: 30/06/11 @ 15:26:13 \| Last updated: 04/07/11 @ 16:51:41 Credits: Carol Lushbough License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow carries out alignments using TCoffee and ClustalW2 for a set of non-redundant proteins where the starting point is a particular genomic coding sequence representing only one member of the gene family in a given species. For the BioExtract Server implementation, the necessary steps for accomplishing this task involve: 1. Selecting the NCBI tblastx tool and providing the accession number of the known nucleotide sequence record as input. 2. The output from ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 3 times Tags (7): alignment \| gene \| genomic \| proteins \| sequence \| species \| workflow	View Download (v1)