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Items tagged with "gi" (8)

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Workflows (8)

Workflow Simplify a BLAST text file (2)

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.

Created: 2007-10-03 | Last updated: 2009-07-28

Workflow Sequence_or_ID_or_GI (1)

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.

Created: 2008-06-07

Credits: User Hamish McWilliam

Attributions: Workflow Structure_or_ID

Workflow EBI_PICR_Sequence_to_UniParc_and_InterPro (2)

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...

Created: 2008-06-08 | Last updated: 2008-06-08

Credits: User Hamish McWilliam

Attributions: Workflow EBI_dbfetch_UniParc Workflow EBI_Fetch_InterPro_Matches_UniParc Workflow EBI_PICR_Sequence_to_ID

Workflow EBI_PICR_Sequence_to_ID (1)

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.

Created: 2008-06-08

Credits: User Hamish McWilliam

Workflow Extract proteins using a gi - output as fa... (1)

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.

Created: 2010-03-19

Credits: User Ian Laycock Network-member nclteamc

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

  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...

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: User Ian Laycock Network-member nclteamc

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

Workflow Retrieve Genome Seqn using gi nos (1)

Retrieves the genome seqn for both the target and source strains using gi nos

Created: 2010-03-19

Credits: User Ian Laycock Network-member nclteamc

Workflow NCBI Gi to Kegg Pathway Descriptions (5)

This workflow accepts a list of NCBI gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2012-01-12 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft

Attributions: Workflow NCBI Gi to Kegg Pathways

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Non-Information Resource URI: http://www.myexperiment.org/tags/603

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