title: MTGIpick allows robust identification of genomic islands from a single genome.
abstract: 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.
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.|Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA.
authors.forename: Qi
authors.initials: Q
authors.lastname: Dai
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
authors.forename: Chaohui
authors.initials: C
authors.lastname: Bao
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
authors.forename: Yabing
authors.initials: Y
authors.lastname: Hai
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
authors.forename: Sheng
authors.initials: S
authors.lastname: Ma
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhou
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
authors.forename: Cong
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA.
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA.
authors.forename: Wenwen
authors.initials: W
authors.lastname: Huo
authors.affiliation: College of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Liu
authors.affiliation: College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Yao
authors.affiliation: Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA.
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Xuan
authors.affiliation: Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75080, USA.
authors.forename: Min
authors.initials: M
authors.lastname: Chen
authors.affiliation: Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA.|Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing, 100084, China.
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation; D012984:Software