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ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes. The gitlab pages associated with this repository is the source to the custom DNS https://icescreen.migale.inrae.fr which is an alias of ip 147.100.164.89 (pages.mia.inra.fr). This DNS was set in settings/pages -> new domain (https://forgemia.inra.fr/ices_imes_analysis/icescreen_documentation/pages). The request for the custom DNS was asked by adminforgemia.

**Main features of ICEscreen**

- Detection of signature proteins (SPs) of ICEs/IMEs by using blastP on a curated resource.	BlastP allows for an accurate assignment of hits to a given ICE/IME superfamily or family. The curated resource was derived from an analysis of over 120 ICEs and IMEs in Streptococcus genomes by the DINAMIC lab.
- Detection of distant homologs of SPs by using HMM profiles of ICEs/IMEs protein families. The HMM profiles have been either imported from trusted resources or created and curated when needed.
- Detection of the ICE/IME structures: ICEScreen groups together SPs that belong to the same ICE/IME structures to the best of its ability.
- Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation.

**Main Output files**

There are 3 main output results files generated by ICEscreen:

- Detected Signature Proteins table (`*_detected_SP_withMEIds.csv`): list of the signature proteins detected by the tool and their possible assignment to an ICE or IME element. It is a comma separated table of 48 columns with a one line header. Each line represents a signature protein detected by ICEscreen.
- Detected ICEs/IMEs table (`*_detected_ME.tsv`): list of the ICEs and IMEs elements detected by the tool, including information about the signature proteins they contain. It is a tab separated table of 21 columns, the header is at line #3. Information in this file is similar to the output file _withICEIMEIds.csv (option -m) but centered around a list of ICE / IME structures instead of a list of SPs.
- Results summary (`*_detected_ME.summary`): this file summarizes the main parameters and statistics regarding the ICE / IME structures and the SPs.

**Installing/running ICEscreen**

To install and run ICEscreen locally or on a Galaxy instance, see  https://icescreen.migale.inrae.fr/run_icescreen/.
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**Citation**

ICEscreen is developed by J. Lao, T. Lacroix, C. Coluzzi, G. Guédon, N. Leblond-Bourget and H. Chiapello from the University of Lorraine DynAMic and the INRAE MaIAGE research teams. Thank you for citing our latest publication, see https://icescreen.migale.inrae.fr for details.