Main Output files

There are 4 main output files generated by ICEscreen, they can found in the directory ICEscreen_results/results/detection_ME/:

• *_detected_SP_withMEIds.tsv: List of the signature proteins detected by the tool and their possible assignment to an ICE or IME element.
• *_detected_ME.tsv: List of the ICEs and IMEs elements detected by the tool, including information about the signature proteins they contain.
• *_detected_ME.summary: Statistical summary by category of result.
• *_detected_ME.log: Parameters used by ICEscreen to generate the results.

The file *_detected_SP_withMEIds.tsv

This file lists the signature proteins detected by the tool and their possible assignment to an ICE or IME element. It is a comma separated table with a header. Each line represents a signature protein detected by ICEscreen.

Description of the columns

Information associated with the ICE/IME element detected by ICEscreen

Information extracted from the GenBank annotation

Information on BlastP results

Information on raw BlastP results and BlastP results enriched with ICEscreen annotation

Information on the results obtained with HMM

File *_detected_ME.tsv

This file lists the ICEs / IMEs / partial elements structures detected by the tool including the SPs they contain. It is a tab separated table with a header. Information in this file is similar to the output file _withICEIMEIds.tsv (option -m) but centered around a list of ICE / IME structures instead of a list of SPs. The identifiers for the CDSs reported in this file are the locus tag if present or [Protein identifier]-[CDS start position] if not (in case of gbff file wih multiple genome records, the genome identifier is added like so [Genome identifier]-[Protein identifier]-[CDS start position].

Description of the columns

File *_detected_ME.summary

This file summarizes the main parameters and statistics regarding the ICE / IME structures and the SPs. The parameters section includes the maximum number of CDSs between subsequent SPs in the same segment and the maximum number of CDSs between subsequent SPs for an IME. The general statistics are on (1) the number of elements detected and their type, (2) the number of signature proteins detected, their type and their relationship with a mobile element, and (3) the segments and their content. Example of statistics includes “Total number of segments”, “Number of segments with one element”, “Number of segments with several elements”, “Number of segments with nested elements”, “Number of segments with no element”, “Number of complete ICE (4 types of SP)”, etc. If multiple genomes are stored back to back in a gbff file, the summaries for each genome identifiers are displayed back to back according to their order in the original genbank file.

File *_detected_ME.log

This file contains the detailed internal parameters and algorithms (step by step) used by ICEscreen to generate the results.

Detailled architecture of the ICEscreen output folder, including intermediate files

All the files generated by the different steps of ICEscreen are stored in a folder named ICEscreen_results. Below is the folder’s content:

└── ICEscreen_results/
    ├── faa/
    |   └── *.faa
    └── results/
        └── <genbank name>/
            ├── detection_ME/
            |   ├── *_detected_ME.log
            |   ├── *_detected_ME.summary
            |   ├── *_detected_ME.tsv
            |   └── *_detected_SP_withMEIds.tsv
            ├── detection_SP/
            |   ├── Blast_mode/
            |   |   ├── blastp_output/
            |   |   ├── filtered_results/
            |   |   ├── unfiltered_results/
            |   |   └── *_blast_SP.tsv
            |   ├── hits_cleaning/
            |   |   ├── proteins_to_remove/
            |   |   ├── *_detected_SP_hmm_cleaned.tsv
            |   |   ├── *_detected_SP_hmm_cleaned_reannotated.tsv
            |   |   ├── *_detected_SP_source.faa
            |   |   └── *__detected_SP_source.tsv
            |   ├── HMM_mode/
            |   |   ├── filtered_results/
            |   |   ├── hmmscan_output/
            |   |   ├── unfiltered_results/
            |   |   └── *_hmm_SP.tsv
            |   └── *_detected_SP.tsv
            ├── visualization_files/
            |   ├── *_icescreen.embl
            |   ├── *_icescreen.gb
            |   ├── *_icescreen.gff
            |   ├── *_source.fa
            |   └── *_source.gff
            └── icescreen.conf

Here is the details about each output folders and files:

• faa
  • *.faa: Multifasta of the protein products annotated in the genbank files.
• results: All results of ICEscreen.
  • detection_ME: this folder include the final results files, see the section on the main output files.
  • detection_SP: Files generated by the first step of the pipeline which detects the signature proteins. The signature proteins detected in this step are stored in the files *_detected_SP.tsv. Each row corresponds to a detected signature protein.
  • visualization_files: Files that allow to visualize the ICEscreen results in a genome visualization software. Tested with Artemis, JBrowse, and IGV. Only SPs of mobile elements that are not to be manually reviewed can be visualized.
    • *_source.fa: FASTA sequence of the genome in genbank file.
    • *_source.gff: GFF3 file with annotation extracted from genbank file.
    • *_icescreen.gff: Results of ICEscreen: the mobile elements and signature proteins detected are annotated in GFF3 format.
    • *_icescreen.embl: Results of ICEscreen: the mobile elements and signature proteins detected are annotated in EMBL format. This format is recommended with Artemis.
    • *_icescreen.gb: original genbank file modified with the addition of the results of ICEscreen (the mobile elements and signature proteins detected) in genbank format.
  • icescreen.conf: Config file with absolute paths of all inputs and outputs files used by the ICEscreen pipeline. Parameters of each step are also provided.