MTGIpick allows robust identification of genomic islands from a single genome

作者：Qi Dai, Chaohui Bao, Yabing Hai, Sheng Ma, Tao Zhou, Cong Wang, Yunfei Wang, Wenwen Huo, Xiaoqing Liu, Yuhua Yao, Zhenyu Xuan, Min Chen, Michael Q. Zhang · 发表于：Briefings in Bioinformatics · 年份：2016 · DOI：10.1093/bib/bbw118 · 被引用次数：65 · 研究领域：Genomics and Phylogenetic Studies、Probiotics and Fermented Foods、RNA and protein synthesis mechanisms

Genomic islands (GIs) that are associated with microbial adaptations and carry sequence patterns different from that of the host are sporadically distributed among closely related species. This bias can dominate the signal of interest in GI detection. However, variations still exist among the segments of the host, although no uniform standard exists regarding the best methods of discriminating GIs from the rest of the genome in terms of compositional bias. In the present work, we proposed a robust software, MTGIpick, which used regions with pattern bias showing multiscale difference levels to identify GIs from the host. MTGIpick can identify GIs from a single genome without annotated information of genomes or prior knowledge from other data sets. When real biological data were used, MTGIpick demonstrated better performance than existing methods, as well as revealed potential GIs with accurate sizes missed by existing methods because of a uniform standard. Software and supplementary are freely available at http://bioinfo.zstu.edu.cn/MTGI or https://github.com/bioinfo0706/MTGIpick.