Doglas Parise

Abstract Dealing with genomic mobility is a complex task for current predictors. With an increasing number of sequencing genomes, there is a constant demand for software that can handle multiple inputs. Considering this, we present the Genomic Island Prediction Software 2 (GIPSy2), a new version of well-established software for predicting bacterial genomic islands and mobilome.

Introduction Bacterial genomes are small and compact; on average, 88% of their genomes consist of coding genes.1 Consequently, the ability to regulate gene expression in diverse environments is crucial for stabilizing cell homeostasis and adapting to environmental challenges.2 Computational systems biology uses Gene Regulatory Networks (GRNs) to understand the mechanisms that coordinate the shifts in gene expression and to represent the transcriptional gene regulation of organisms.

Abstract The number of draft genomes deposited in Genbank from the National Center for Biotechnology Information (NCBI) is higher than the complete ones. Draft genomes are assemblies that contain fragments of misassembled regions (gaps). Such draft genomes present a hindrance to the complete understanding of the biology and evolution of the organism since they lack genomic information. To overcome this problem, strategies to improve the assembly process are developed continuously.