Computational methods for predicting genomic islands in microbial genomes.
Clusters of genes acquired by lateral gene transfer in microbial genomes, are broadly referred to as genomic islands (GIs). GIs often carry genes important for genome evolution and adaptation to niches, such as genes involved in pathogenesis and antibiotic resistance. Therefore, GI prediction has gradually become an important part of microbial genome analysis. Despite inherent difficulties in identifying GIs, many computational methods have been developed and show good performance. In this mini-review, we first summarize the general challenges in predicting GIs. Then we group existing GI detection methods by their input, briefly describe representative methods in each group, and discuss their advantages as well as limitations. Finally, we look into the potential improvements for better GI prediction.
Department of Computer Science, National University of Singapore, 13 Computing Drive, Singapore 117417, Republic of Singapore.
Bingxin
B
Lu
Department of Computer Science, National University of Singapore, 13 Computing Drive, Singapore 117417, Republic of Singapore.
Hon Wai
HW
Leong
Comparative genomics; Genome segmentation; Outlier detection; Pathogenicity islands; Sequence composition