Finally we got an end-to-end structural annotation tool for phages!

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

"Writers have been using me long before the advent of AI. I am the punctuation equivalent of a cardigan—beloved by MFA grads, used by editors when it’s actually cold, and worn year-round by screenwriters. I am not new here."

My colleague asked me to circulate this job posting for Professor / Associate Professor in Computational Biology / Genomics at the University of Tokyo (P.S. I'm not affiliated): www.k.u-tokyo.ac.jp/en/informati...

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

Unicore is now published on GBE 🚀 Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n 📃 doi.org/10.1093/gbe/evaf109

Introducing our invited speaker for the session on 'Viral Dark Matter' we have Rachel Seongeun Kim from the Seoul National University!!!! The registrations for on-site & remote participation are still open! More info: RdRp.io #RdRpSummit2025

I'm presenting a poster about Metabuli, a metagenomic taxonomic classifier leveraging both DNA and protein sequences, at #RECOMB2025! Please come and share yout thoughts!

Visit our posters at #RECOMB2025 for: Structural: MSAs, Virus DB, Core Genes, Motif Discovery, Multimer Clustering & Search, pLM Foldseek, Environmental analysis Metagenomics: Classification & Metabuli App GPU-based & RNA search, Proteome clustering, Novel Ribozyme discovery & get Marv stickers!

@eunbelivable.bsky.social presented our viral protein structure database BFVD, including the new V2 update with improved predictions using 12 recycles for higher quality structures. Check out the paper and data here: 📄 academic.oup.com/nar/article/... 🌐 bfvd.foldseek.com #RECOMB2025

I also updated the main #RECOMB2025 things-to-do map to include more tourist attractions and some of the standout vegan places I have visited myself (except the two places next to Yonsei, which I didn't have a chance to visit yet): www.google.com/maps/d/edit?...

Finding vegetarian and vegan food in Korea can be tricky. I added a mini-guide to the #RECOMB2025 things-to-do site with some resources. Let me know if you want more recommendations! recomb.org/recomb2025/t...

Congratulations to @imartayan.bsky.social and @curiouscoding.nl whose paper on fast minimizer computation with simd has been accepted to SEA 2025 🙌🏻 www.biorxiv.org/content/10.1...

Big Fantastic Virus Database (BFVD) version 2 improves 31% of predictions through 12 ColabFold recycles. PAEs and MSAs now also available for download and in the webserver. 🌐https://bfvd.foldseek.com 💾https://bfvd.steineggerlab.workers.dev/ 1/3

🚀 New Metabuli DB is out! It includes quality-filtered GTDB R220, RefSeq viruses, and the human T2T. Prokaryotes follow the GTDB taxonomy; viruses and the human genome use NCBI taxonomy. Download it and expand with genomes of your choice using "updateDB" command. metabuli.steineggerlab.workers.dev

Just published simd-sketch, a crate for fast bucket sketches. It's 7x to 30x faster than BinDash, by using the simd-minimizers crate for fast hashing, and a nearly branch-free implementation. Here's a blogpost with a survey of minhash history & methods, and evals: curiouscoding.nl/posts/simd-s...

Metabuli App preprint is out! 💻Taxonomic classification & interactive visualization—right on your laptop 🛠️Create new databases or update existing ones with new sequences. 🧵1/5 github.com/steineggerla... www.biorxiv.org/content/10.1101/2025.03.10.642298v1

MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT 📄 biorxiv.org/content/10.1... 💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶

Easy taxonomic profiling with the Metabuli App! Explore your samples with publication-ready Sankey and Krona plots. We accelerated Metabuli further, classifying 2x22M reads vs. GTDB in just 43 min on a MacBook Pro M2. 🧵1/4 🚀https://github.com/steineggerlab/Metabuli-App