Accurate Microbial Genome Annotation Using an Integrated and User-Friendly Environment for Community Expertise of Gene Functions: The MicroScope Platform

Abstract

The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of the thousands of genomes stored in public databanks. The reference databases and computational methods that constitute the basis of automatic genome annotation pipelines are constantly evolving: firstly, the annotation of single genomes can now be performed through simultaneous analysis of multiple genomes in a comparative context; secondly, the focus of genome annotation has been extended to the reconstruction of genome-scale metabolic networks that allow for a more comprehensive overview of the functional capabilities of the organism under study. Starting from the results of structural, functional and relational annotation pipelines, MicroScope provides an integrated environment for the annotation and comparative analysis of prokaryotic genomes, by combining tools and graphical interfaces for genome analysis and manual curation of gene annotations in a comparative genomics context. In the present chapter, we discuss the different stages of annotation using the MicroScope platform, and, through examples of degradation pathways in bacterial species, we illustrate some of the functionalities that are useful for improving the quality of automatic genome annotations. Thus, we demonstrate that integrated environments such as MicroScope clearly contribute to maintaining accurate resources, through the help of the user community.

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

“…each time a new method is integrated into PkGDB, a corresponding data set is added in the ‘Search by Keywords’ functionality and in the gene editor) and (iii) synteny results and metabolic network predictions, the combination of which can be very helpful in formulating hypotheses on the biological function of non-annotated genes (22) (Figure 1). To facilitate the exploration and curation process, the MicroScope analysis tools are organized in a menu bar which is detailed in Vallenet et al.…”

“…For this purpose, integrative capabilities of the MicroScope platform (comparative tools, queries, etc.) can be used to refine and improve gene annotation in a metabolic context (21,22). …”