Identifying the Origin of Replication in a Pseudomonas Megaplasmid

Background

My project revolves around a cryptic plasmid 1Mb in size found in the plant pathogen Pseudomonas syringae.  The plasmid appears to have various costs associated with its acquisition among Pseudomonads.  Due to its costs I sought to conjugate the plasmid into the clincally relevant P. aeruginosa to observe similar costs.  However, among all Pseudomonads tested P. aeruginosa is the only strain unable to uptake the plasmid.  I am now looking at the reasons why this may be, one of which includes host range.  To tackle this portion of my project I need to ID the origin of replication and engineer a minimal plasmid with this origin.  To find the origin of replication two methods are generally used.  These are GC skew to ID a broad region and motif repetition to ID ori genes with AT rich regions.  I will utilize custom software programs to tackle these two problems.

Concept Map 

Git Hub Repository

My Github

Red Flags

To Do

-Python script for finding repetitive motifs
-BLAST regions where repetitive motifs occur
-Packaging
-User friendly polishing