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

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,...

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Autores principales: Liu, Meng, Li, Xiaobin, Xie, Yingzhou, Bi, Dexi, Sun, Jingyong, Li, Jun, Tai, Cui, Deng, Zixin, Ou, Hong-Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323972/
https://www.ncbi.nlm.nih.gov/pubmed/30407568
http://dx.doi.org/10.1093/nar/gky1123
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author Liu, Meng
Li, Xiaobin
Xie, Yingzhou
Bi, Dexi
Sun, Jingyong
Li, Jun
Tai, Cui
Deng, Zixin
Ou, Hong-Yu
author_facet Liu, Meng
Li, Xiaobin
Xie, Yingzhou
Bi, Dexi
Sun, Jingyong
Li, Jun
Tai, Cui
Deng, Zixin
Ou, Hong-Yu
author_sort Liu, Meng
collection PubMed
description 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.
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spelling pubmed-63239722019-01-10 ICEberg 2.0: an updated database of bacterial integrative and conjugative elements Liu, Meng Li, Xiaobin Xie, Yingzhou Bi, Dexi Sun, Jingyong Li, Jun Tai, Cui Deng, Zixin Ou, Hong-Yu Nucleic Acids Res Database Issue 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. Oxford University Press 2019-01-08 2018-11-08 /pmc/articles/PMC6323972/ /pubmed/30407568 http://dx.doi.org/10.1093/nar/gky1123 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Liu, Meng
Li, Xiaobin
Xie, Yingzhou
Bi, Dexi
Sun, Jingyong
Li, Jun
Tai, Cui
Deng, Zixin
Ou, Hong-Yu
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements
title ICEberg 2.0: an updated database of bacterial integrative and conjugative elements
title_full ICEberg 2.0: an updated database of bacterial integrative and conjugative elements
title_fullStr ICEberg 2.0: an updated database of bacterial integrative and conjugative elements
title_full_unstemmed ICEberg 2.0: an updated database of bacterial integrative and conjugative elements
title_short ICEberg 2.0: an updated database of bacterial integrative and conjugative elements
title_sort iceberg 2.0: an updated database of bacterial integrative and conjugative elements
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323972/
https://www.ncbi.nlm.nih.gov/pubmed/30407568
http://dx.doi.org/10.1093/nar/gky1123
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