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D-JRP14-WP3.D1 MGE database

Johansson, Markus

In WP3 of Full Force, it was planned to develop, evaluate and make available a database of MGEs detection from single isolates and metagenomics datasets. In research performed by Markus H K Johansson (DTU, DK), this databases was established and consists of ∼4450 MGE sequences that originate from ∼1050 different species. They contain several types of mobile elements:

  • Insertion sequences (ISs) are among the smallest types of iMGEs. They are often composed of a transposase gene flanked by two inverted repeats (IRs). They are notable for their ability to modulate gene expression and promote mobility by forming composite transposons (ComTns), translocatable units (TUs) and in the case of elements from the IS26 family pseudo-composite transposons (PCTs).
  • Unit transposons (Tns) are generally flanked by IRs and carry a transposase gene. They usually carry a resolvase gene, accessory genes and/or additional iMGEs.Miniature Inverted Repeats (MITEs) are non-autonomous ISs or Tns that have undergone deletions in their core genes but have retained the IR and can form ComTn-like structures.
  • Integrative Conjugative Elements (ICEs), Cis-Mobilizable Elements (CIMEs) and Integrative Mobilizable Elements (IMEs) are larger iMGEs capable of conjugation. They can either conjugate independently or be co-mobilized by conjugation of other elements. These elements carry many accessory genes and other MGEs.

A command line version of MobileElementFinder is designed to run either on your local machine or inside a docker container, and is made publicly available at https://pypi.org/project/MobileElementFinder/ and https://github.com/bhattlab/MGEfinder

 

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