Description

iLund4u is a bioinformatics tool designed for the search and annotation of accessory genes and hotspots across large proteome datasets. This web application focuses on iLund4u's protein annotation mode, enabling users to determine whether homologues of a query protein are encoded within variable islands and hotspots.
It can help in protein function prediction by applying principles such as guilt by association, and co-localisation.

Source code available at the GitHub Page.

We also recommend visiting the tool's detailed documentation website that provides an algorithm description, example-driven guide, and documentation to the command-line version and python API.
See our preprint: Egorov et al. bioRxiv, 2024

Currently only protein mode is available as web tool.

iLund4u pipeline


Databases

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

Submission form

Amino acid sequence in fasta format or just as a sequence (without >id line; can be multiple lines). MMseqs2 will be run to find homologues in the iLund4u database.
Optional arguments
iLund4u database to perform searching.
Feature label to show for homologous proteins.
Report hotspots that are flanked by conserved genes on only one side (located on the end of non-circular sequences).
MMseqs search query coverage cutoff in search for homologous proteins. Allowed values: [0:1].
MMseqs search target coverage cutoff in search of homologous proteins. Allowed values: [0:1].
MMseqs search fident (fraction of identical matches) cutoff in search of homologous proteins. Allowed values: [0:1].
Run parameters
Please, enter your e-mail address to receive your results link.
Will be used in output folder name.

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


Authors & Contact

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

Please contact us by e-mail or use GitHub Issues to report any technical problems related to iLund4u. You can also use Discussions section for sharing your ideas or feature requests!