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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.

SUBMITTER: Dai Q 

PROVIDER: S-EPMC6454522 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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MTGIpick allows robust identification of genomic islands from a single genome.

Dai Qi Q   Bao Chaohui C   Hai Yabing Y   Ma Sheng S   Zhou Tao T   Wang Cong C   Wang Yunfei Y   Huo Wenwen W   Liu Xiaoqing X   Yao Yuhua Y   Xuan Zhenyu Z   Chen Min M   Zhang Michael Q MQ  

Briefings in bioinformatics 20180501 3


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 robu  ...[more]

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