An Efficient Approach to Explore and Discriminate Anomalous Regions in Bacterial Genomes Based on Maximum Entropy

Abstract

Abstract

Recently, there has been an increase in the number of whole bacterial genomes sequenced, mainly due to the advancing of next-generation sequencing technologies. In face of this, there is a need to provide new analytical alternatives that can follow this advance. Given our current knowledge about the genomic plasticity of bacteria and that those genomic regions can uncover important features about this microorganism, our goal was to develop a fast methodology based on maximum entropy (ME) to guide the researcher to regions that could be prioritized during the analysis. This methodology was compared with other available methods. In addition, ME was applied to eight different bacterial genera. The methodology consists of two main steps: processing the nucleotide sequence and ME calculation. We applied ME to Xanthomonas axonopodis pv. citri 306 (XAC) and Xanthomonas campestris pv. campestris ATCC 33913 (XCC), both of which have their anomalous regions well documented. We then compared our results against those from Alien Hunter, HGT-DB, Islander, IslandPath, and SIGI-HMM. ME was shown to be superior in terms of efficiency and analysis duration. Besides, ME only needs the genome sequence in FASTA format as input. The proposed strategy based on ME is able to help in bacterial genome exploration. This is a simple and fast strategy for individual genomes in comparison with other available methods, without relying on previous annotation and alignments. This methodology can also be a new option in the early stages of analysis of newly sequenced bacterial genomes.