ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions
Brendan King, Terry Farrah, Matthew A. Richards, and 3 more authors
Bioinformatics (Oxford, England), May 2018
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) at probannoweb.systemsbiology.net, and as a local python package implementation (ProbAnnoPy) at github.com/PriceLab/probannopy. CONTACT: evangelos.simeonidis@systemsbiology.org or nathan.price@systemsbiology.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.