FirmiData is a set of 40 public annotated genomes of Firmicutes (information on strains are available in Table 1, ‘Data file 41’, [9]). These genomes were extracted from the Refseq database for which ICEs and IMEs annotation was added using the standard annotation features and qualifiers used in the Genbank format [9].

The search for ICEs and IMEs relies on data from the literature and on a semi-automated procedure that was described in [1] and [2]. All annotations were carefully checked and corrected when necessary and almost all of these elements were delineated at the nucleotide level.

ICE expert annotation is based on the identification of genes carried by their conjugation module and encoding three proteins (relaxase, coupling protein and VirB4) needed for their transfer. ICE identification also relies on the search of three types of integrases (tyrosine integrases, serine integrases, and DDE transposases of the ISLre2 family). IME characterization was done in a similar fashion as for ICEs except that we searched for genes carried by their mobilization modules encoding a relaxase and eventually a coupling protein.

The co-localization of the genes encoding the signature proteins attests for the presence of an ICE or an IME. Their boundaries were then searched. One relevant information for the ICE/IME delineation is the knowledge of the insertion site targeted by their integrase. To get this information, phylogenetic analyses were done to identify the closest integrase for which the integration site was already identified. ICE/IME boundaries were identified manually by the search for the Direct Repeats (DRs) flanking the elements. When the DRs were missing, too short or too degenerated to be detected, the region containing the element was compared with (i) target regions or genes lacking elements, or (ii) already known and well-delineated elements.

When an expected signature gene was not identified within an element, a thorough examination of all its genes and sequences was done to identify those encoding the missing signature proteins.

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