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how to add plasmids

asked 2016-06-09 16:45:38 -0500

ybukhman gravatar image

The pgdb that I am interested in has a bacterium's chromosome but does not have plasmids. How do I add plasmids to it?



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answered 2016-06-09 17:22:02 -0500

Suzanne Paley gravatar image

Bring up the PathoLogic window (Tools -> PathoLogic) and invoke the command Build -> Specify Replicons. This will allow you to add additional replicons (you will need to supply a separate annotation file and optional sequence file for each one). After you have done this, you should run a Trial Parse on the added replicons, and then run the Automated Build again to incorporate the data from the new replicons into the PGDB. The Automated Build command should ignore the chromosome from which the PGDB was previously built (although it will of course incorporate enzymes from the chromosome when it rescores pathways). However, I believe it has been a long time (years) since anyone has run it in this way, to add a replicon to a previously built PGDB, so there could potentially be issues that we are not aware of. Please let us know how it goes.


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Thanks! In addition to adding plasmids, we also need to add a number of new genes to the chromosome and edit its sequence. Would it be better for us to generate a new PGDB from scratch? The old PGDB is Tier 3. Does it contain any info that would not be automatically regenerated if we build our own?

ybukhman gravatar imageybukhman ( 2016-06-13 16:20:24 -0500 )edit

I doubt you will lose anything by creating your own pgdb so long as you run all the refinement steps (e.g. pathway hole filler, transport inference, transcription unit prediction). Depending on when the old pgdb was built, you will likely even benefit from improvements to pathologic and metacyc.

Suzanne Paley gravatar imageSuzanne Paley ( 2016-06-13 16:44:26 -0500 )edit

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Asked: 2016-06-09 16:45:38 -0500

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Last updated: Jun 09 '16