ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.
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ICEberg 2.0：细菌整合和接合元件的更新数据库
DOI：
10.1093/nar/gky1123
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发表时间：
2019-01-08
影响因子：
14.9
通讯作者：
Ou HY
中科院分区：
文献类型：
--
作者：
Liu M;Li X;Xie Y;Bi D;Sun J;Li J;Tai C;Deng Z;Ou HY
摘要 ICEberg 2.0（http://db-mml.sjtu.edu.cn/ICEberg/）是一个更新的数据库，提供有关细菌整合和接合元件（ICE）的全面信息。与之前的版本相比，主要做了三点改进。首先，借助文本挖掘和人工管理，它现在记录了 1032 个 ICE 的详细信息，其中 270 个有实验支持，762 个来自生物信息学预测。其次，随着越来越多的证据表明，ICE经常动员所谓的“搭便车者”，例如整合和可动员元素（IME）和顺式可动员元素（CIME），49个IME和7个CIME之间的83种已知的转移相互作用以及从文献中摘取的19个ICE被包括在内，并用视觉直观的有向图进行说明。还添加了 260 个染色体携带的 IME 和 235 个 CIME 的扩展集合。最后，ICEberg 2.0提供了一个在线工具ICEfinder来预测细菌基因组序列中的ICE或IME。它结合了整合酶、松弛酶和/或 IV 型分泌系统的相似性搜索以及这些相应同源基因的共定位。通过最近的更新，ICEberg 2.0 可能为理解 ICE 的生物学特性提供更好的支持，特别是因为它们与同源可移动元件的相互作用可能进一步促进水平基因流动。
Abstract ICEberg 2.0 (http://db-mml.sjtu.edu.cn/ICEberg/) is an updated database that provides comprehensive information about bacterial integrative and conjugative elements (ICEs). Compared with the previous version, three major improvements were made. First, with the aid of text mining and manual curation, it now recorded the details of 1032 ICEs, including 270 with experimental supports and 762 from bioinformatics prediction. Second, as increasing evidence has shown that ICEs frequently mobilize the so-called ‘hitchhikers’, such as integrative and mobilizable elements (IMEs) and cis-mobilizable elements (CIMEs), 83 known transfer interactions between 49 IMEs and 7 CIMEs with 19 ICEs taken from the literature were included and illustrated with visually intuitive directed graphs. An expanded collection of 260 chromosome-borne IMEs and 235 CIMEs was also added. At last, ICEberg 2.0 provides an online tool ICEfinder to predict ICEs or IMEs in bacterial genome sequences. It combines a similarity search for the integrase, relaxase and/or type IV secretion system and the co-localization of these corresponding homologous genes. With the recent updates, ICEberg 2.0 might provide better support for understanding the biological traits of ICEs, especially as their interaction with cognate mobilizable elements may further promote horizontal gene flow.