Metabuli App v1.2 makes Metabuli easier to use on desktop! Run taxonomic profiling, curate databases, and visualize results locally. 🚀 No command line, no server setup, no internet required. Download the app from github.com/steineggerla...
Our pre-built RefSeq, HGRM2, and HROM databases have Kraken2/Braken counterparts. You can use these Braken databases directly alongside Metabuli to estimate species abundance.
Please check the docs: jaebeom-kim.github.io/metabuli-doc...
Metabuli now features three layers of mismatch tolerance: synonymous DNA mutations, conservative amino acid substitutions, and substitutions in joker positions. Additionally, we've introduced E-value-based filtering to discard noisy matches.
Metabuli & Metabuli App v1.2 improve novel species classification with higher precision and recall. New light mode is 1.8× faster and requires 50% less storage while keeping precision. New RefSeq, GTDB, HRGM, and HROM databases added.
💾 github.com/steineggerla...
📄 doi.org/10.64898/2026.03.13.711249
45 novel protein folds in the updated AFESM (AFDB + ESMatlas) manuscript:
• 12 high-confidence folds in AFESM
• 33 by ColabFold-repredicting 2.3M low-quality domains
We show AFDB captures most domains already and ESMfold struggles with novelty
🌏 afesm.foldseek.com
📄 biorxiv.org/content/10.1...
As an organizer, it was great to see such a large student participation! As a metagenomics researcher, learning about reference microbiome/virome was very helpful to my studies.
<RSG Korea 2026 1st Webinar>
Human Reference Microbiome for the Era of Microbiome Medicine
Prof. Insuk Lee (Yonsei University)
March 24th, 2026, 17:00-18:00 (KST)
Register here: docs.google.com/forms/d/e/1F...
The Zoom link will be emailed before the webinar.
#Microbiome #Metagenomics
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
Huge congratulations and thanks to
@sunjaelee.bsky.social, @milot.bsky.social,
@cameron.gilchrist, and @martinsteinegger.bsky.social 👍
Curate your database. 🧵4/5
- GTDB, NCBI, ICTV, or custom taxonomy supported.
- Add genomes to a pre-built DB to save time (benchmark in figure)
- Expand taxonomy. e.g., integrate ICTV viruses into a GTDB prokaryote DB.
⏱️Building a DB of 8,520 GTDB species took 106 min on a MacBook M2 Pro (32G)
Explore results with interactive visualization. 🧵3/5
- Generate customized Sankey plots.
- Search for taxa of interest.
- Filter by classified reads or proportion.
- Click taxon nodes for subtree views.
- Extract reads classified to a taxon.
- Access NCBI Taxonomy and genome browser.
The app runs desktop-optimized Metabuli. 🧵2/5
Classifying 2X22M human gut reads vs. 36K genomes over 8,465 species took:
🖥️46 min on a Windows desktop (i9-9900, 32GB RAM)
💻39 min on a MacBook M2 Pro (32GB RAM)
Easy and interactive taxonomic profiling with Metabuli App.
It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop.
No command line, server, or internet required.
Now published in Bioinformatics! 🧵1/5
doi.org/10.1093/bioi...
github.com/steineggerla...
Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#
New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....
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
죽고 싶지만 떡뽂이는 먹고싶어!
