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Items tagged with "gi" (9)

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Workflows (9)

Taverna 1 Original Uploader Paul Fisher	Simplify a BLAST text file (v2) Created: 03/10/07 @ 18:36:06 \| Last updated: 28/07/09 @ 13:01:45 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simply pass in the string the SAME as the port name, e.g. seq_id, p, per etc. Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 357 times \| Downloaded: 140 times Tags (11): bioinformatics \| BLAST \| gene identifier \| gi \| matrix \| sequence \| similarity \| simple \| simplifier \| substitution \| summary	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_PICR_Sequence_to_ID (v1) Created: 08/06/08 @ 14:03:07 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Map a protein sequence to the known identifiers of identical sequences. Uses the EBI's PICR web service (see http://www.ebi.ac.uk/Tools/picr/) to perform the mapping. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 72 times \| Downloaded: 39 times Tags (9): bioinformatics \| ebi \| gi \| picr \| protein \| sequence identifier \| uniparc \| uniprot archive \| upi	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: 32 times \| Downloaded: 18 times Tags (2): gi \| 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: 150 times \| Downloaded: 58 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: 26 times \| Downloaded: 10 times Tags (5): FASTA \| genome \| gi \| nucleotide \| sequence	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	NCBI Gi to Kegg Pathway Images (v2) Created: 12/01/12 @ 09:38:10 \| Last updated: 12/01/12 @ 15:04:00 Credits: Katy Wolstencroft Paul Fisher Attributions: NCBI Gi to Kegg Pathways License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 12 times Tags (6): genbank \| genes \| gi \| image \| ncbi \| pathways	View Download (v2)
Taverna 2 Original Uploader Katy Wolstencroft	NCBI Gi to Kegg Pathway Descriptions (v2) Created: 12/01/12 @ 09:46:31 \| Last updated: 12/01/12 @ 14:54:37 Credits: Katy Wolstencroft Attributions: NCBI Gi to Kegg Pathways License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 6 times \| Downloaded: 8 times Tags (8): bconv \| genbank \| gene \| genes \| gi \| ncbi \| pathway \| pathways	View Download (v2)