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Thomas Lacroix authored
v1.3.3: The output file structure has been modified to prepare for the integration of new modules. The output files themselves do not change but their locations on disk do. See [this section of the documentation](https://icescreen.migale.inrae.fr/interpret_results/description_output_files) for more details ; The documentation now mentions how to install miniforge3 and informs on miniconda3 licencing updates ; The following conda dependencies were added to prepare for the integration of new modules: pyarrow, bash, decorator, scipy ; The following conda dependencies were upgraded: biopython =1.85, pandas >=2.2, snakemake-minimal >=8, and blast =2.16 ; Bug fixes [Issue #19](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/19) Wrongly reported as duplicate locusTag. Caused by reannot_XerS: the dataframe data was accessed instead of the dataframe df. ; Bug fixes [Issue #20](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/20) RuntimeError: Error in IsThereAnIntegraseBetweenThoseTwoConjModule: unrecognized positioning ofICEsIMEsStructureOne. This error happens when 2 relaxases are neighbors on the genome and one of them is found by blastp only while the other one is found by HMM only. ; Bug fixes [Issue #21](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/21) RuntimeError: Error in fillUpColocalizedOtherICEsIMEsStructures: ICEsIMEsStructureIT_mostUpstreamStart == -1. In EMStructure.py->listSPsIsContainedWithinOtherStructure, added a parameter to ignore the absence if an SPType was represented in EMStructureToCompareSent. ; Bug fixes [Issue #22](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/22) RuntimeError: Error in fillUpColocalizedOtherICEsIMEsStructures: self_mostUpstreamStart == -1. fillUpColocalizedOtherICEsIMEsStructures was not checking for the case when 2 SP of the same type are part of a tuplet. ; Bug fixes [Issue #23](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/23) ValueError: End location must be greater than or equal to start location. Cause : method reannot_XerS: df[CDS_num] == i was used instead of df[CDS_num] == CDS_numTarget. ; Bug fixes [Issue #24](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/24) splitListOrderedSPs colocalizeByMaxNumberCDS distanceWithNextSp. Cause : error while reverting a integrase false positive to metadata of the second best blast hit. ; Bug fixes [Issue #25](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/25) TypeError: < not supported between instances of SP and SP. Cause: def lt(self, other) was not implemented for the object class. ; Bug fixes [Issue #26](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/26) ValueError End location. Cause : mishandling of CDS features end location for SP that are re-annotated. ; Bug fixes [Issue #27](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/27) Adding Relaxase family domain of most similar ref SP Type Tyrosine integrase. ; Bug fixes [Issue #28](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/28) Another case of splitListOrderedSPs colocalizeByMaxNumberCDS. Cause: wrong command line in Error in rule detect_mobile_elements. ; Bug fixes [Issue #29](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/29) SP to SeqFeature error. Cause : Biopython error due to misformating of SP matrice in the blastp step.
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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 Bacillota genomes.

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 DynAMic lab at Nancy.
  • 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.

Documentation and Usage

The full documentation is available at https://icescreen.migale.inrae.fr.

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.

External links