The Atkinson Lab Server Portal

Welcome! Here we provide access to our online tools and services.

Online tools

iLund4u

iLund4u is a bioinformatics tool for search and annotation of accessory genes and hotspots in a large set of proteomes. With web version you can find whether homologues of your query protein are encoded in variable islands and hotspots.

webFlaGs

Predicting protein functional association in microbial and viral genomes by analysis of conservation of genomic context (Flanking Genes).

uORF4u

A bioinformatics tool for conserved uORF annotation in 5′ upstream sequences of a user-defined protein of interest or a set of protein homologues. It can also be used to find small ORFs within a set of nucleotide sequences.

MSA4u

A simple visualisation tool for Multiple Sequence Alignments.
Supported input: Multiple sequence alignments or unaligned sequences in fasta format.

Databases

NetFlax

Interactive NetFlax (Network-FlaGs for toxins and antitoxins) predicted toxin-antitoxin pairs interface with structural predictions.

VAD Network

Web interface for exploring structural clusters in the Viral AlphaFold Database. Includes structural predictions, sequence and structure clusters, and metadata with hits to protein sequence and structure databases.

Contact

The Atkinson lab Home Page

We are located at the BMC as part of the Faculty of Medicine, Lund University, Sweden 🇸🇪

Mailing address:
Gemma Atkinson
BMC, Lund University
Sölvegatan 17, C13, 223 62 Lund, Sweden

You can also contact us by e-mail:

Gemma C. Atkinson, Group Leader
gemma.atkinson(at)med.lu.se

Artyom A. Egorov, PhD student and developer
artem.egorov(at)med.lu.se (for technical questions)

Server news & updates

- VAD network is now online.

- iLund4u web version is updated and now connects your results to the accessory protein database.

- First version of iLund4u web version is available supporting protein search against iLund4u databases.

- New NetFlax-predicted toxin-antitoxin pairs interface is now available.

- Updated webFlaGs is now available.

- First release is now online; Currently uORF4u and MSA4u are available; new version of webFlaGs is under construction.