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Draft genome & pathologic

asked 2017-09-19 02:37:24 -0600

jo gravatar image

What do you think is the best practice when reconstructing a metabolic network using pathwaytools/pathologic and having only a draft genome?

Draft genomes can have a lot of unconnected contigs. Pathologic needs a annotation file as input but the annotation of draft genomes is also not always trustworthy.

I'm interested in this because I encountered different results of predicted reactions and pathways when I created two pgdbs out of the same genome but using two distinct annotation files done by different prokka versions. I know that the pathway prediction algorithm is doing some kind of text mining with the annotation file but it is also using the raw sequence data to annotate gene function itself.

What is the balance between text mining and redoing the annotation? Can this be changed for draft genomes? Do you have recommendation for annotation software which works best with pathologic? (prokka, rast, ... ?)

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answered 2017-09-21 01:38:26 -0600

Suzanne Paley gravatar image

Pathologic does not do any sequence annotation, itself. The only time it uses the raw sequence data is to run the Pathway Hole Filler (a manual refinement step that relies on you having a fairly good set of pathways predicted in the first place). The database pathologic produces will only be as good as the annotation you provide. I'm sorry, I don't know enough about the various annotation programs to be able to recommend one over another.

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Asked: 2017-09-19 02:37:24 -0600

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Last updated: Sep 21