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Description

iLund4u is a bioinformatics tool for search and annotation of accessory genes and hotspots in a large set of proteomes.

Supported input: gff3 for annotation files (prokka/pharokka generated); fasta for protein sequences
Programming language: Python3
OS: MacOS, Linux
Python dependencies: biopython, bcbio-gff, scipy, configs, pandas, matplotlib, seaborn, progess, leidanalg, igraph. pyhmmer, msa4u, lovis4u
Python version: >= 3.8
OS-level dependencies: MMseqs2 (included in the package)
License: WTFPL
Version: 0.0.10 (December 2024)

Workflow

pipeline

What you can do with iLund4u

  • Cluster up to millions of genomes based on proteome composition similarity
  • Annotate core and accessory genes within each cluster
  • Identify and annotate genomic islands
  • Annotate the functions of accessory proteins encoded within islands
  • Cluster genomic islands to identify variability hotspots
  • Get visualisation of clusters and hotspots with our LoVis4u library

Installation

  • iLund4u can be installed directly from pypi:
python3 -m pip install ilund4u
  • The development version is available at github :
git clone https://github.com/art-egorov/ilund4u.git
cd ilund4u
python3 -m pip install --upgrade pip
python3 -m pip install setuptools wheel
python3 setup.py sdist
python3 -m pip install .

! If you're a linux user, run ilund4u --linux post-install command once to update paths in the premade config files that set by default for MacOS users.

Databases

db_fig

iLund4u has two precomputed databases of hotspots built on phage and plasmid sequences.
The database of phages was built based on running hotspot annotation mode on all available PhageScope database sequences (~870K genomes, version of September 2024). For plasmids database we took IMG/PR database of plasmids (~700K sequences, version of June 2024).

To download iLund4u database from our server you can use the following argument: --database <phages|plasmids>. For example, to get plasmids database you need to run:

ilund4u --database plasmids

Database sizes (compressed): Phages: 6.48GB; Plasmids: 1.07GB

Reference

If you find iLund4u useful, please cite:
Artyom. A. Egorov, Vasili Hauryliuk, Gemma C. Atkinson, Systematic annotation of hyper-variability hotspots in phage genomes and plasmids, bioRxiv 22024.10.15.618418; doi: 10.1101/2024.10.15.618418

Contact

Please contact us by e-mail artemdotegorovATmeddotludotse or use Issues to report any technical problems.
You can also use Discussions section for sharing your ideas or feature requests!

Authors

iLund4u is developed by Artyom Egorov at the Atkinson Lab, Department of Experimental Medical Science, Lund University, Sweden. We are open for suggestions to extend and improve iLund4u functionality. Please don't hesitate to share your ideas or feature requests.