From @gbouras13.bsky.social & colleagues in @plos.org #Computational #Biology | Thirteen quick tips for bacteriophage genome annotation | I like all Tips, but particularly TIP | #Bioinformatics #Education #PLOSCBQT #Virus #Genomics #Biocuration | 🧬🖥️🧪🔓🦠 🇦🇺🇨🇦 🇪🇬🇺🇸 ⬇️ journals.plos.org/ploscompbiol...

Thirteen quick tips for bacteriophage genome annotation

journals.plos.org

🚨 New preprint 🚨 We’ve discovered millions of viruses from sequencing data but we don’t always know who they infect. Our new tool, VHAMSTeR generates broad virus host predictions across the tree of life (prokaryote, plant, animal, fungi and protist hosts) A thread 🧵👇 www.biorxiv.org/content/10.6...

Viral host assignment across the tree of life with VHAMSTeR

Viruses infect organisms across the tree of life, but many are not associated with a specific host. Here we present VHAMSTeR (Virus Host Assignment Model using Sequence Transformers and Reading-frames...

biorxiv.org

LoL-align is out in @natmethods.nature.com! It aligns protein structures without superposition. More sensitive than TM-align and DALI, producing better alignments 5–20× faster. Now available in Foldseek! 📄 www.nature.com/articles/s41... 💾 github.com/steineggerlab/foldseek 🌐 search.foldseek.com

Skani (github.com/bluenote-157...) is now v0.4.0! Big performance update: **~2.5x faster** and ~30-40% less RAM for average nucleotide identity (ANI) comparison of genomes. The database format has changed (breaks forward compatibility; watch out!).

GitHub - bluenote-1577/skani: Fast average nucleotide identity (ANI) calculator for bacterial genomes, MAGs, and contigs. Supports genome comparisons and large-scale database searches.

Fast average nucleotide identity (ANI) calculator for bacterial genomes, MAGs, and contigs. Supports genome comparisons and large-scale database searches. - bluenote-1577/skani

github.com

A new preprint 🎉 from phagefoundry.org Mycobacteriophages are candidate therapies for drug-resistant mycobacterial infections, but we still don't know how most of them get into their hosts. Our new preprint tackles this challenge 👉🏽 www.biorxiv.org/content/10.6...

Very happy to share that HIDEN-SEQ is now out in @natmicrobiol.nature.com! Using this technique, we recapitulated decades of established phage genetics and uncovered new gene functions, including previously unknown anti-defense factors against several defense systems. www.nature.com/articles/s41...

AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions. 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...

BFVD v3 contains 5.8M viral protein structures, 16× more than v2; 75% high quality, filling a major gap in AFDB coverage. It fully covers 72.6% of reference proteomes and spans 72.7% of ICTV species. Great work by @eunbelivable.bsky.social et al. 📄 www.biorxiv.org/content/10.6... 🌐 bfvd.foldseek.com

Introducing highly experimental localfold.org Building on @martinsteinegger.bsky.social af2 webgpu port, @milot.bsky.social optimizations & jax ports of af3-like models by @marielle.bsky.social, Choonghwan Lee, Julia Buhmann. WARNING: runs directly on your 💻, may drain 🪫 & eat data📱 & overheat 🔥💻

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 2mo ago

Run AlphaFold2 locally in your browser via WebGPU, no installation needed, it's just a static webpage using your own GPU or CPU. Short proteins run in seconds. Larger ones are still slow: a 291-aa protein takes ~7 minutes on my M4 Pro. ❗It's just a PoC. 🌐 martin-steinegger.github.io/alphafold2-w...

The PhD and Postdoc application links are now live! Come join me at UNIL to work on deep learning for protein structure, interactions & design. pickybinders.org#open-positions

Janani Durairaj (Jay)@ninjani.bsky.social · 2mo ago

Some exciting news: I'm joining the University of Lausanne @unil.bsky.social @dbc-unil.bsky.social as an Assistant Professor next month 🎉 My group will work on context-aware deep learning for protein structure, interaction & design. Postdoc and PhD openings coming soon - keep an eye out!

ColabFold 1.6.3 is out! 2.5x faster, pip-installable, ipSAE+pDockQ2 scores. Thanks Choonghwan Lee, Marielle Russo, Gyuri Kim 🐍pip install colabfold[alphafold] CF2 Sneak Peak with AF3/Boltz/Protenix/ESMFold2… 🐍pip install "colabfold[alphafold3]@git+https://github.com/sokrypton/ColabFold@af3-preview"

The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)

🧬 Postdoc ad is now live: evolutionary genomics of Klebsiella pneumoniae phages. How do prophage depolymerases vs SGNH-esterases shape phage host range? Krakow, Poland. Deadline 21 Sept: mostowylab.com/job-postdoc-...

Run AlphaFold2 locally in your browser via WebGPU, no installation needed, it's just a static webpage using your own GPU or CPU. Short proteins run in seconds. Larger ones are still slow: a 291-aa protein takes ~7 minutes on my M4 Pro. ❗It's just a PoC. 🌐 martin-steinegger.github.io/alphafold2-w...

Happy to see the last parts of my PhD with @milja001.bsky.social now published in @microbiomej.bsky.social (many thanks to all involved!) link.springer.com/article/10.1...

Distinct gut viral communities across life stages in dairy cattle - Microbiome

Background Ruminant gut microbial communities influence host health, productivity, and methane emissions, yet viral communities across life stages remain uncharacterized. Whilst bacteriophages shape m...

link.springer.com

Ryan Cook@ryancook94.bsky.social · last yr.

🧬🐄 NEW PREPRINT: Really happy to finally share the last big piece of work from my PhD! Spoiler: Cows are great and so are their viromes 🧵1/13 www.biorxiv.org/content/10.1...

Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 www.biorxiv.org/content/10.6... 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com

So happy to share that this work is finally out, now in @nature.com! Lots of new goodies since preprint so plz check it out (old thread below). Giant thank you to everybody involved + all @savitski-lab.bsky.social and @typaslab.bsky.social lab members 🙏🙏🙏 @embl.org nature.com/articles/s41...

Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature

The&nbsp;T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.

nature.com

Tara Bartolec@tarabartolec.bsky.social · 2y ago

1/11 - With Karin Mitosch and Clément Potel + colleagues in Savitski lab and @typaslab.bsky.social @embl.org, I’m very happy to share our discovery of a hyper-promiscuous phage protein kinase (T7K) which broadly deactivates bacterial defenses! 🦠 www.biorxiv.org/content/10.1...

Always nice to see Somerton Man resurface. I guess I'm one of the few who've looked at his DNA a few years back. We got the mitochondrial haplotype (already known) and got real close to the chrY haplotype too. Ran out of time & then someone else finished the job. www.indailysa.com.au/inreview/mus...

Tamám Shud: Phoebe Bridgers is the latest artist inspired by Somerton Man mystery - InReview | InDaily, Inside South Australia

Phoebe Bridgers' new album joins a long list of artists inspired by the 70-year-old Adelaide mystery – even after it was apparently solved.

indailysa.com.au

@gbouras13.bsky.social talking about his new protein structure-based bacterial genome annotation tool, Baktfold. 🧫🧬 GitHub: github.com/gbouras13/ba... Preprint: www.biorxiv.org/content/10.6... #ISME20

Excited to be talking about my #phage #bioinformatics tool #Phables to study #viral #ecology in #IBD-associated #metagenomes. Come check out my talk in session AS13 at 2.30pm on Tuesday 18th Aug in room 303-305. #ISME20 GitHub: github.com/Vini2/phables Publication: academic.oup.com/bioinformati...

GitHub - Vini2/phables: 🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes - Vini2/phables

github.com

We're having fun developing post-cloud bioinformatics tools: reimagining some of the bioinformatics canon as local, browser-native applications so your data never has to leave your laptop. Here's the first set: edwards.flinders.edu.au/viz/ Let us know if you want other tools local to your laptop

-viz

Welcome to the -viz suite of tools: classic bioinformatics tools, reimagined for the browser. agviz · bamviz · genbankviz · phispyviz Each of our tools is a classic bioinformatics tool, but reimagi…

edwards.flinders.edu.au

If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out Thanks to @ardc.edu.au for making this possible!

If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out Thanks to @ardc.edu.au for making this possible!

I am excited to share that our manuscript titled 'Defining the ESKAPE pathogen prophage repertoire with PHORAGER' is now available online as a preprint in BioRxiv! 🤩 (doi.org/10.64898/202...) Here we present PHORAGER, a Nextflow pipeline for the identification and quality assessment of prophages 🧬

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

We are hosting the 2026 @abacbs.bsky.social conference at RMIT University City Campus Melbourne on 16-20 Nov 2026. Hope to see you there.

Polypolish v0.7.1 is out! github.com/rrwick/Polyp... Main new feature is better handling of read name suffixes, which makes it easier to use Polypolish with aligners other than BWA-MEM. I've been using it with minibwa, which seems pretty great: github.com/lh3/minibwa

GitHub - rrwick/Polypolish: a short-read polishing tool for long-read assemblies

a short-read polishing tool for long-read assemblies - rrwick/Polypolish

github.com

New blog post! I reran the Autocycler paper benchmarks on some new tools/versions/pipelines: rrwick.github.io/2026/07/24/b... (1/3)