Rapid Annotation of Photosynthetic Systems (RAPS): automated algorithm to generate genome-scale metabolic networks from algal genomes

Abstract Algae have great potential to serve as platform strains for engineering efforts, but tools for these species lag behind traditional model systems like E. coli and yeast. Metabolic models are one such tool that would enhance our ability to rationally engineer algae, but current automated algorithms to build models do not perform well for algal genomes. We present a novel software pipeline, Rapid Annotation of Photosynthetic Systems (RAPS), which leverages manual curation efforts of published models to create high quality first draft metabolic networks for new species. We compared models produced by our pipeline to published models and found that these models are able to capture more genes than the published models and are more predictive of experimentally determined growth rate. We used RAPS to automate the creation of 8 first draft metabolic models of new species to enable the further study of metabolism in these species.