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

Summary 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. Availability and Implementation 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 . Contact http://[email protected] ; http://[email protected]