Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

Metabuli GTDB232 database is now available. Try this to classify your metagenomc reads using 199,923 GTDB species, NCBI RefSeq viruses, and a human T2T genome. jaebeom-kim.github.io/metabuli-doc...

Results of the first ICTV Computational Virus Taxonomy Challenge are out! Metabuli was among the most accurate and fastest classifiers evaluated. doi.org/10.64898/202... Try Metabuli App, a desktop GUI for DB curation, read QC, classification, and visualization: jaebeom-kim.github.io/metabuli-doc/

First community challenge for automated virus taxonomy

The rapid rate of virus discovery renders manual curation by taxonomy experts increasingly impractical, creating a need for reliable software that can reproducibly assign viral contigs to taxa at all ...

doi.org

Does your designed active site already exist in nature? Is an uncharacterized protein hiding a catalytic site or a pocket? Folddisco answers both, searching millions of structures for a 3D motif in seconds. @natbiotech.nature.com 🧬 📄 www.nature.com/articles/s41... 🧵1/7👇

Structural motif search across the protein universe with Folddisco - Nature Biotechnology

Folddisco enables protein structural motif search in million scale databases.

nature.com

Structural motif search across the protein universe with Folddisco - @martinsteinegger.bsky.social go.nature.com/4g8lCb0

Structural motif search across the protein universe with Folddisco - Nature Biotechnology

Folddisco enables protein structural motif search in million scale databases.

go.nature.com

Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv. Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen) github.com/bluenote-157... 1/6

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2mo ago

Sensitive long-read amplicon sequence variant recovery with savont https://www.biorxiv.org/content/10.64898/2026.05.26.727271v1

Surprised to discover that Thermo Fisher appears to show a fake western blot for the validation of one of their p53 antibodies. I've added a diagram to show the very similar bands. This does not appear to be one of the "published figures" but their own internal data.

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@rsg-korea.bsky.social · 4mo ago

We successfully concluded the RSG Korea webinar on March 24, 2026. "Human Reference Microbiome for the Era of Microbiome Medicine" was presented by Professor Insuk Lee (Yonsei University). Thank you to Professor Lee, and all participants for making this event a success.

<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... 🧬💻

A new gateway to global antimicrobial resistance data

New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.

ebi.ac.uk

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...

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!

George Bouras@gbouras13.bsky.social · 12mo ago

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...

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...

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

biorxiv.org

"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."

The Em Dash Responds to the AI Allegations

“In recent months, a curious fixation has emerged in corners of academia: the em dash. More specifically, the apparent moral panic around how it is...

buff.ly

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...

Call for applications (professor or associate professor), Department of Computational Biology and Medical Sciences (Deadline Sep 30) ｜Job Opportunities｜Information｜Graduate School of Frontier Scienc...

Call for applications (professor or associate professor), Department of Computational Biology and Medical Sciences (Deadline Sep 30) ｜Job Opportunities｜Information｜GSFS offers both master‘s and doct...

k.u-tokyo.ac.jp

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!

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · last yr.

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!

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?...

RECOMB2025 Things to do - Google My Maps

RECOMB2025 Things to do

google.com

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...

RECOMB 2025 - Things to do

RECOMB 2025 - Seoul, South Korea

recomb.org

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...

SimdMinimizers: Computing random minimizers, fast

Motivation Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller ...

biorxiv.org

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