This workflow uses one or more services that are deprecated as of 31st December 2012 (about 11 years ago), and may no longer function. Show details...

Compare genome, extract proteins which are drug targets, apply to KEGG pathway

Created: 2010-03-19 13:16:24      Last updated: 2010-03-19 13:33:53

 

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 against another formatdb database created from existing drug targets (provided by user). Finds proteins that are similar between pathogenic proteins and existing drug targets. Feeds the GI numbers of these proteins into KEGG. Workflow produces image of KEGG pathways which protein is involved in. Also outputs final list of interesting proteins, pathway and KEGG descriptions, url of image (from KEGG database).

Information Preview

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/1172/download?version=1
[ More InfoExpand ]


Information Workflow Components

Information Authors (2)
Information Titles (2)
Information Descriptions (1)
Information Dependencies (0)
Inputs (16)
Processors (9)
Beanshells (14)
Outputs (10)
Datalinks (36)
Coordinations (6)

Information Workflow Type

Taverna 2

Information Uploader

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (2)

(People/Groups)

Information Attributions (3)

(Workflows/Files)

Information Tags (7)

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

 

Citations (0)

None


Version History

In chronological order:



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (1)

Log in to make a comment

  • Thursday 21 April 2011 15:59:01 (UTC)

    This is a very nice workflow. Very educational. It just needs some fiddling to become more directly applicable to the world. Just to give an example, there is a string with the value D:\blast\bin\formatdb.exe.

    My suggestion is to split the workflow in many smaller ones, e.g. into those nested embedded ones shipping with it.

     




Workflow Other workflows that use similar services (93)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.


Workflow Triplify namespace list from global search... (1)

Thumb
No description

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Workflow Cow-Human Ortholog Pathways and Gene annot... (2)

Thumb
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. As the Cow genome is currently unfinished, the workflow subsequently maps the cow ensembl gene ids to human orthologues. Entrez and UniProt identifiers are then identified...

Created: 2007-10-03 | Last updated: 2009-12-03