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ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions

By Brendan King, Terry Farrah, Matthew Richards, Michael Mundy, Evangelos Simeonidis, Nathan D. Price

Posted 16 Jun 2017
bioRxiv DOI: 10.1101/151258 (published DOI: 10.1093/bioinformatics/btx796)

Gap-filling is a necessary step to produce quality genome-scale metabolic reconstructions capable of flux-balance simulation. Most available gap-filling tools use an organism-agnostic approach, where reactions are selected from a database to fill gaps without consideration of the target organism. Conversely, our likelihood based gap-filling with probabilistic annotations selects candidate reactions based on a likelihood score derived specifically from the target organism's genome. Here, we present two new implementations of probabilistic annotation and likelihood based gap-filling: a web service called ProbAnnoWeb, and a standalone python package called ProbAnnoPy. Our tools are available as a web service with no installation needed (ProbAnnoWeb), available at http://probannoweb.systemsbiology.net, and as a local python package implementation (ProbAnnoPy), available for download at http://github.com/PriceLab/probannopy.

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