ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

• Published in: Nucleic acids research 2019-01, Vol.47 (D1), p.D660-D665
• Main Authors: Liu, Meng, Li, Xiaobin, Xie, Yingzhou, Bi, Dexi, Sun, Jingyong, Li, Jun, Tai, Cui, Deng, Zixin, Ou, Hong-Yu
• Format: Article
• Language: English
• Subjects: Bacterial Secretion Systems - genetics; Database Issue; Databases, Genetic; DNA Transposable Elements; Genome, Bacterial; Genomics - methods; Regulatory Sequences, Nucleic Acid; Sequence Alignment - methods; Software
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gky1123

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.