merlinv4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models

Abstract

ABSTRACTGenome-scale metabolic models have been recognized as useful tools for better understanding living organism’s metabolism.Merlin(https://merlin-sysbio.org/) is an open-source and user-friendly resource that hastens these models’ reconstruction process, conjugating manual, and automatic procedures, while leveraging user’s expertise with a curation-oriented graphical interface. An updated and redesigned version ofmerlinis herein presented. Since 2015, several features were implemented inmerlin, along with profound changes in the software architecture, operating flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates led to an increase in the user-base, resulting in multiple published works including genome metabolic (re-)annotation and model reconstruction of multiple (lower and higher) eukaryotes and prokaryotes.