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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).

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  • 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.


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