Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.
Bioinformatics. 2018 Jul 1;34(13):2161-2167. doi: 10.1093/bioinformatics/bty095.
Genomic islands (GIs) are clusters of genes of probable horizontal origin that play a major role in bacterial and archaeal genome evolution and microbial adaptability. They are of high medical and industrial interest, due to their enrichment in virulence factors, some antimicrobial resistance genes and adaptive metabolic pathways. The development of more sensitive but precise prediction tools, using either sequence composition-based methods or comparative genomics, is needed as large-scale analyses of microbial genomes increase.
IslandPath-DIMOB, a leading GI prediction tool in the IslandViewer webserver, has now been significantly improved by modifying both the decision algorithm to determine sequence composition biases, and the underlying database of HMM profiles for associated mobility genes. The accuracy of IslandPath-DIMOB and other major software has been assessed using a reference GI dataset predicted by comparative genomics, plus a manually curated dataset from literature review. Compared to the previous version (v0.2.0), this IslandPath-DIMOB v1.0.0 achieves 11.7% and 5.3% increase in recall and precision, respectively. IslandPath-DIMOB has the highest Matthews correlation coefficient among individual prediction methods tested, combining one of the highest recall measures (46.9%) at high precision (87.4%). The only method with higher recall had notably lower precision (55.1%). This new IslandPath-DIMOB v1.0.0 will facilitate more accurate studies of GIs, including their key roles in microbial adaptability of medical, environmental and industrial interest.
IslandPath-DIMOB v1.0.0 is freely available through the IslandViewer webserver {{http://www.pathogenomics.sfu.ca/islandviewer/}} and as standalone software {{https://github.com/brinkmanlab/islandpath/}} under the GNU-GPLv3.
Supplementary data are available at Bioinformatics online.
基因组岛（GIs）是基因簇，其可能具有水平起源，在细菌和古菌基因组进化和微生物适应性方面发挥主要作用。由于其富含毒力因子、一些抗生素耐药基因和适应性代谢途径，它们具有很高的医学和工业价值。随着对微生物基因组的大规模分析增加，需要开发更敏感但更精确的预测工具，这些工具可使用基于序列组成的方法或比较基因组学。
IslandViewer 网络服务器中的主要 GI 预测工具 IslandPath-DIMOB 现在已经通过修改确定序列组成偏差的决策算法以及相关移动基因的 HMM 配置文件的基础数据库得到了显著改进。使用比较基因组学预测的参考 GI 数据集和文献综述中手动整理的数据集评估了 IslandPath-DIMOB 和其他主要软件的准确性。与以前的版本（v0.2.0）相比，此 IslandPath-DIMOB v1.0.0 的召回率和精确度分别提高了 11.7%和 5.3%。在测试的单个预测方法中，IslandPath-DIMOB 具有最高的马修斯相关系数，结合了最高的召回率之一（46.9%）和高精确度（87.4%）。唯一具有更高召回率的方法精度明显较低（55.1%）。此新的 IslandPath-DIMOB v1.0.0 将促进更准确地研究 GIs，包括它们在医学、环境和工业感兴趣的微生物适应性中的关键作用。
IslandPath-DIMOB v1.0.0 可通过 IslandViewer 网络服务器{{http://www.pathogenomics.sfu.ca/islandviewer/}}免费获得，也可作为独立软件{{https://github.com/brinkmanlab/islandpath/}}在 GNU-GPLv3 下获得。
补充数据可在《生物信息学》在线获得。
