Improved genomic island predictions with IslandPath-DIMOB.
Improved genomic island predictions with IslandPath-DIMOB.
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DOI：
10.1093/bioinformatics/bty095
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发表时间：
2018-07-01
期刊：
影响因子：
--
通讯作者：
Brinkman FSL
中科院分区：
文献类型：
--
作者：
Bertelli C;Brinkman FSL
基因组岛（GI）是可能水平起源的基因簇，在细菌和古细菌基因组进化和微生物适应性中起着重要作用。由于它们富含毒力因子、某些抗菌素抗性基因和适应性代谢途径，因此具有很高的医学和工业价值。随着微生物基因组大规模分析的增加，需要开发更灵敏但更精确的预测工具，无论是基于序列组成的方法还是比较基因组学。IslandPath-DIMOB是IslandViewer网络服务器中领先的GI预测工具，现已通过修改决策算法以确定序列组成偏差以及相关迁移率基因的HMM概况的基础数据库而得到显著改进。IslandPath-DIMOB和其他主要软件的准确性已使用比较基因组学预测的参考GI数据集以及文献综述中手动整理的数据集进行了评估。与之前的版本（v0.2.0）相比，IslandPath-DIMOB v1.0.0在召回率和精确率方面分别提高了11.7%和5.3%。在测试的各个预测方法中，IslandPath-DIMOB具有最高的马修斯相关系数，结合了最高的召回率（46.9%）和高精度（87.4%）。唯一一种召回率较高的方法的准确率明显较低（55.1%）。这个新的IslandPath-DIMOB v1.0.0将促进对地理标志的更准确的研究，包括它们在医学，环境和工业利益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GNU-GPL v3下的独立软件{{https：//github.com/brinkmanlab/islandpath/}}获得。 补充数据可在Bioinformatics在线获得。
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.
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Islandviewer 4：扩展了大规模数据集基因组岛的预测。
影响因子：
14.9
作者：
Bertelli C;Laird MR;Williams KP;Simon Fraser University Research Computing Group;Lau BY;Hoad G;Winsor GL;Brinkman FSL
通讯作者：
Brinkman FSL
影响因子：
3
作者：
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3
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影响因子：
11.3
作者：
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通讯作者：
Crook DW
影响因子：
3
作者：
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通讯作者：
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