oriTfinder: a web-based tool for the identification of origin of transfers
in DNA sequences of bacterial mobile genetic elements |
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Bacterial mobile genetic elements (MGE), such as integrative and conjugative elements (ICEs) and conjugative plasmids,
have been highlighted as important vehicles for dissemination of pathogenesis and antimicrobial-resistance determinants.
The conjugative regions of the self-transmissible MGE typically consist of four modules: origin of transfer site (oriT), relaxase gene,
gene encoding type IV coupling protein (T4CP) and gene cluster for bacterial type IV secretion system (T4SS).
The oriT region, usually tens to even hundreds of base pairs in length,
contains a conserved nick region (nic) and pairs of inverted repeats (IRs).
Here oriTfinder is designed to facilitate rapid detection of oriTs in bacterial MGE sequences,
especially in the antimicrobial-resistant plasmids and the virulence plasmids.
Citation: X. Li, Y. Xie, M. Liu, C. Tai, J. Sun, Z. Deng, H.Y. Ou (2018) oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. Nucleic Acids Research, 46(W1):W229–W234. doi: 10.1093/nar/gky352. |
Current version: 1.1 | Since: May 2017 |
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