iiinova — where your digital self keeps evolving

Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 23/09/2026

Excited to release LOSAT v0.1.0, a miniaturized reimplementation of the NCBI BLAST algorithm!🧬🚀 Current features: ✅ Supports BLASTN, BLASTP, & TBLASTX ✅ Multithread #Wasm compatible 📦 Now available on #Bioconda! Repo: github.com/satoshikawat... #Bioinformatics #Genomics

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 05/07/2026

#gbdraw v0.13.0 is out! 🎉 Highlights: ✅ Undo/redo support in the web app ✅ Ctrl/Shift/drag-based feature selection ✅ Reproducible CLI commands from the GUI ✅ New `orthogroup_top` label mode ✅ Interactive SVG Gallery tutorials Try it out: gbdraw.app #bioinformatics #genomics #virology

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 27/06/2026

#gbdraw v0.12.1 is now live with a massive update! Powerful new features are now available in your local environment: You can now generate circular comparisons (homology rings) and interactive SVG files directly on your machine 🧬 #bioinformatics #genomics

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 26/06/2026

#gbdraw webapp now supports interactive SVG output! You can click, search, and copy features directly from your browser. Check out the gallery: gbdraw.app/gallery/ #bioinformatics #genomics #microbiology #virology

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 26/05/2026

Circular genome comparison is now live in #gbdraw! 🚀 The built-in LOSATN instantly runs pairwise alignments and generates homology rings for your sequences, 100% in your browser! Try it out: gbdraw.app #bioinformatics #genomics #microbiology

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 17/05/2026

おかげさまで、gbdrawのGitHub starsが100個になりました。ありがとうございます!

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Joanna Masel @joannamasel.bsky.social · 16/05/2026

Our paper unpacking "fitness" is out doi.org/10.1093/gene.... How to define fitness depends on what question you ask. Selection acts on organismal vital rates, longer-term outcomes make sense for genetic lineages, models link them. "Invasion fitness" = speed, but sometimes probability matters more.

doi.org

Why there are so many definitions of fitness in models

Abstract. Evolutionary “fitness” is operationalized in many different ways in models. Its role is to quantify that which is favored by natural selection. G

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 12/05/2026

gbdrawのロゴを作りました。広葉樹林の地図記号...ではないです #gbdraw

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 07/05/2026

🧬Collinearity Analysis is here in #gbdraw v0.11.0! You can easily detect and visualize synteny and collinearity blocks using LOSATP. You can instantly align the entire diagram based on a shared ortholog! Try it now: gbdraw.app #bioinformatics #genomics #microbiology

Collinearity analysis of Hepatoplasmataceae, a group of mollicutes associated with isopod crustaceans. Inverted syntenic blocks are colored in dark red.

Synteny of lividomycin-like aminoglycoside biosynthetic gene clusters. The diagrams are aligned based on livE gene (see next figure for the command)

Dialog box for the livE gene in the record BGC0000708. Click "Align" to align the records based on the shared livE orthologs, as seen in the previous figure.

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Rob Edwards @linsalrob.bsky.social · 06/05/2026

Want to find #prophage in your #bacteria genomes? We built PhiSpy a long time ago, and now we've created a new web page for it: linsalrob.github.io/PhiSpyWeb/ Best of all, the data never leaves your computer! #phage #phagesky

linsalrob.github.io

PhiSpyWeb – Browser-based Prophage Prediction

Browser-based prophage prediction using PhiSpy, Pyodide, and WebAssembly

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 04/05/2026

🚀Excited to release ganflu! A serverless web app to predict CDS for all major influenza viruses (IAV, IBV, ICV, & IDV). 🧬Runs entirely in your browser; your data never leaves your machine. 🔗Try it out: ganflu.app #Bioinformatics #Virology #Influenza #OpenScience

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 29/04/2026

gbdraw v0.10.0 webapp is now available!🧬 Major updates: 🔹Depth track support: Visualize your mapping depth simply by uploading samtools depth TSV files. 🔹Multithreaded LOSAT: Parallel execution to speed up multiple sequence comparisons. Check it out: gbdraw.app #bioinformatics #microbiology

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 26/04/2026

It’s one thing to find a duplicate manuscript, but it’s another level of audacity when they cite the original non-English paper they’re copying from. The results and figures were identical

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 09/04/2026

gbdraw: a genome diagram generator for microbes and organelles www.biorxiv.org/content/10.64898/20…

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Naomichi Takemata @naomichitakemata.bsky.social · 09/04/2026

【拡散希望】私も運営に携わらせてもらっているEMBO–MBSJ Laboratory Leadership Forumが6月27日に東京で開催されます！ラボ運営に必要なスキルについて学べる貴重な機会だと思いますので、みなさん是非ご参加ください！

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 07/04/2026

gbdraw v0.9.1 is out now on Bioconda! Easily visualize microbial genomes and enjoy the #gbdraw web app completely offline. 📦 Install via Bioconda: bioconda.github.io/recipes/gbdr... 🌐 Try the online app: gbdraw.app #bioinformatics #genomics #microbiology #visualization

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Paul Carini @uncultured.carinilab.com · 19/03/2026

Is there a consensus for ANI differences associated with Order, Family, or Genus level divergence in bacteria? I'm looking at ~79% ANI between two genomes and am wondering where that falls.

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Mart Krupovic @mkrupovic.bsky.social · 03/03/2026

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 08/03/2026

Big update for #gbdraw! - Multi-record circular plots: Genomes with multiple replicons can now be displayed in a single view! - Advanced linear plots: Focus on regions of interest with granular control over feature selection and color-coding! Try now: gbdraw.app #microbiology #bioinformatics

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Piotr Lukasik @sympiotr.bsky.social · 11/02/2026

Our new paper in @natcomms.nature.com is now online-early! We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets. 🔗 doi.org/10.1038/s414...

The visualization of two bacterial genomes, of 50 and 52kb, representing independent instances of extreme genomic reduction in ancient heritable endosymbionts of planthoppers.

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Genome Biology and Evolution @genomebiolevol.bsky.social · 10/02/2026

Hao et al. present Imagin as a new gene family derived from a Ginger1 DNA transposon domesticated in the common ancestor of malacostracan crustaceans. 🔗 doi.org/10.1093/gbe/evag010 #genome #evolution #TEsky

doi.org

Validate User

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Joost Snijder @joostsnijder.bsky.social · 04/02/2026

We studied how the glycan shield of alphaherpesvirus fusion protein gB mediates host co-receptor interactions. Great work by Sabrina, check it out! www.biorxiv.org/content/10.6...

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Alex Crits-Christoph @acritschristoph.bsky.social · 04/02/2026

Ktedonobacteria are so freaking cool, with 10+ Mbp genomes, interesting morphologies and tons of BGCs

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 27/01/2026

Visualizing pairwise genome comparisons? No need to run BLAST separately anymore! 🧬 #gbdraw has implemented #LOSAT, a WASM-powered Rust reimplementation of BLASTN/TBLASTX. ✅ No local installation ✅ No data transfer (Serverless) Try it here: gbdraw.app

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Asiya Gusa @asiya-gusa.bsky.social · 17/01/2026

Sharing our lab’s first publication! Probing clinical isolates of Cryptococcus, a disease-causing fungus of the lungs and brain, we found multiple heat-mobile elements that ‘jump’ in the genome at body temperature (!) with the ability to drive adaptive changes. journals.plos.org/plosgenetics...

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Evgenii Protasov @evgenii-protasov.bsky.social · 19/01/2026

LPSN continues to be an essential authority on the #taxonomy of #prokaryotes. The depth of information regarding effective/valid publications and type strains is truly unmatched. A well-deserved achievement on becoming an ELIXIR Core Data Resource 👏 #Archaea #Bacteria #OpenScience #MicroSky

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Robert J. Gifford @robjgifford.bsky.social · 19/01/2026

As virus discovery accelerates, integrating new sequences meaningfully is becoming a central challenge. Flavivirus-GLUE provides an open framework for multi-scale comparative genomic analyses of flaviviruses. gluetools.substack.com/p/flavivirus...

gluetools.substack.com

Flavivirus-GLUE

Comparative Genomics Across Evolutionary Scales

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 17/01/2026

𝘐𝘮𝘢𝘨𝘪𝘯: an integrase-like gene conserved across malacostracan crustaceans derived from a Ginger1 DNA transposon We discovered a domesticated transposon in crustaceans, which has abandoned its mobility for a host function (likely reproductive). doi.org/10.1093/gbe/...

Figure 1. Imagin, a multi-exon integrase-like gene in malacostracan crustaceans.
(A) Structure of the PjImagin gene. The transcript is shown in light blue and the CDS in white. The YPYY motif is colored yellow, the H2C2 zinc finger is colored sky blue, the defunct DDE catalytic core is colored in pink, and the disordered region is shaded in gray. Gray vertical lines denote the positions of key residues denoted in panels C and D, with
the last two lines being shaded to indicate the corresponding positions for the lost D and E residues (Panel E).
(B) The genomic context of PjImagin and orthologs. PjImagin is flanked by exons 14 and 15 of methylmalonyl-CoA mutase, mitochondrial-like (MMUT) gene, which runs on the opposite strand. Note that the Imagin gene of the swimming crab (Portunus trituberculatus) lies on an unrelated position. MMUT CDS is colored green, and MMUT exons corresponding to exons 14 and 15 of P. japonicus MMUT are connected with light green ribbons. CDS of other genes are shaded gray.
(C) Domain architectures of malacostracan Imagin proteins. The coloring scheme follows that of panel (A).
(D) Conservation of the YPYY motif and the H2C2 (HHCC) zinc-finger domain in integrase proteins. Species names are listed on the left, with protein accession numbers provided on the right. Entries Ginger1-1_HM, Ginger1-2_HM, and Ginger1-3_HM were adopted from (Bao et al. 2010).
(E) Loss of the DDE catalytic residues in crustacean Imagin proteins. Species names are listed on the left, with protein accession numbers provided on the right. Note that some residues may be missing from this alignment because regions containing long gaps were automatically suppressed by DALI. Each residue is shaded by background color according to the secondary structure assignments by DSSP: light green: loop; dark green: helix; blue: strand. Conserved aspartic acid (D) and glutamic acid (E) residues comprising the DDE motif are highlighted in black.

Figure 3. Imagin is a domesticated Ginger1 DNA transposon.
(A) Maximum-likelihood phylogenetic tree of 121 DDE integrases and derivatives (136 sites; model: VT+R6).
(B) Subtree of (A) showing the phylogenetic relationships of Ginger1-like elements. The bar beside the tree indicates amino acid substitutions per site. The slashed values beside the nodes indicate the support values for the ultrafast bootstrap test followed by the SH-like approximate likelihood ratio test (1,000 trials each).

Figure 2. Phylogenetic analysis of decapod Imagin proteins.
A total of 463 sites were used for the maximum-likelihood phylogenetic analysis using IQTREE v3.0.1 (substitution model: Q.MAMMAL+F+I+G4). The slashed values beside the nodes indicate the support values for the ultrafast bootstrap test followed by the SH-like approximate likelihood ratio test (1,000 trials each). The bar indicates amino acid substitutions per site. Euphausiacea and Stomatopoda were used as the outgroup. Imagin proteins from brachyuran crabs formed a long branch relative to the other taxa, suggesting accelerated evolution following the translocation event in this lineage.

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 16/01/2026

#gbdraw web app update! 🧬✨ 🖱️ Drag & drop elements 🎨 Live edit colors, strokes, titles & canvas 🧫 Bakta & Pharokka presets added! Try it now: gbdraw.app #bioinformatics #genomics #virology #microbiology #bacteriology #visualization

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 26/12/2025

LOSAT - A miniaturized reimplementation of the BLAST algorithm github.com/satoshikawat... The goal is to enable pairwise TBLASTX right in the webapp. Since using the full suite is too heavy, I'm stripping down the algorithm to compile it into Wasm. #Bioinformatics #RustLang #WebAssembly #Genomics

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 18/12/2025

gbdraw v0.8.0 is out! 🚀 - Fully Serverless Web App (Faster & Stable; no file size limit!) - Lighter dependencies - Circular track overlap fixed New URL: gbdraw.app #gbdraw #bioinformatics #genomics #visualization #virology #microbiology #bacteriology

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James McInerney @jomcinerney.bsky.social · 06/12/2025

the program will output multiple support measures for internal branches

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Robert J. Gifford @robjgifford.bsky.social · 04/12/2025

Gardening in the Viral Genome Wilderness: Why virus genomics needs structure, not pipelines. gluetools.substack.com/p/the-sequen...

gluetools.substack.com

Gardening in the Viral Genome Wilderness

Why virus genomics needs structure, not pipelines.

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 28/11/2025

Another server for gbdraw webapp, with a new domain! gbdraw.app

gbdraw.app

Streamlit

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Vijini Mallawaarachchi @vijinim.bsky.social · 25/11/2025

🧬 Come check out my poster on agtools, an open-source Python framework for analysing and manipulating assembly graphs at #ABACBS2025 Poster #106 • 💻 Github: github.com/Vini2/agtools 📄 Preprint: biorxiv.org/content/10.110…

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 24/11/2025

New update for the gbdraw web app!🚀 You can now display gene labels ONLY on the first genome in the linear diagram. Just select "First" in the "Label layout" option. Try it out here👉: gbdraw.streamlit.app #gbdraw #bioinformatics #genomics #visualization #virology #microbiology #streamlit

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Comparative genomics group IRB-BSC Barcelona (PI: Toni Gabaldón) @gabaldonlab.bsky.social · 07/11/2025

#Review: “Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration” in JME We reflect on how data explosion, new structural/AI tools, and complex features impact how we think about orthology link.springer.com/article/10.1...

link.springer.com

Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration - Journal of Molecular Evolution

The rapid advancement of DNA sequencing technologies and computational algorithms has led to an unprecedented surge in genomic data, driven by several large-scale sequencing projects worldwide. Orthol...

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 04/11/2025

宿主細胞からATPとリボソームをチューチュー吸い取る寄生細菌がいても僕は驚かない

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 04/11/2025

Given that even metabolism can be outsourced, I wouldn’t be surprised if a cellular organism existed that had abandoned the ribosome; the final distinction between a cell and a virus might then lie in the dichotomy between growth–fission and synthesis–assembly

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 30/10/2025

gbdraw v0.7.0 is now available on the bioconda channel! I also posted some recipes for viral genome diagrams on the GitHub Discussion thread. Hope you find them useful: github.com/satoshikawat... #gbdraw #bioinformatics #genomics #visualization #virology #microbiology

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Anna Dewar @annadewar.bsky.social · 08/01/2025

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social

rdcu.be

A phylogenetic approach to comparative genomics

Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 26/10/2025

🚀gbdraw v0.7.0 is out! - Feature overlap resolution - Gradated BLAST hit ribbons - Ruler-style scale - Top/bottom legend placement - Optimized defaults (for small genomes) Try out: 👉 gbdraw.streamlit.app #gbdraw #bioinformatics #genomics #visualization #virology

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 09/10/2025

🚀 Released gbdraw v0.6.0! - Added dinucleotide skew plotting to linear mode. Fixed the bug where only GC skew could be drawn. - Added links to relevant sections of the documentation throughout the web app help menu. Try out:👉 gbdraw.streamlit.app

A grid of 12 circular E. coli genome maps showing dinucleotide skew plots for GC, CG, AG, GA, CT, TC, TG, GT, CA, AC, AT, and TA. Each circle displays color-coded genome annotations (CDS, rRNA, tRNA, etc.) around the outer ring, with inner line plots showing positive and negative dinucleotide skew values.
Below the grid, a linear representation of two E. coli genomes shows annotated tracks, GC content, and GC skew plots, with two genomes linked with ribbons representing BLASTN hits. Note that the lower track (pathogenic strain O157:H7 Sakai) has multiple prophage insertions (shaded with orange) that are absent from the upper track (the laboratory strain K-12). Further below are five linear genome comparison diagrams of Hepatoplasmataceae mollicutes, each with colored gene annotations, GC content and GC skew plots, and gray ribbons indicating TBLASTX hits across genomes.

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 29/09/2025

Released gbdraw v0.5.3! 🚀 - Smarter layout engine: reduced overlapping labels, legends, or definitions (linear mode) - Circular mode: genomes >5 Mb now show tick labels in megabases (Mb) - Official Documentation published with full guides & tutorials 🔗 gbdraw.streamlit.app

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Zamin Iqbal @zaminiqbal.bsky.social · 25/09/2025

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 25/09/2025

令和７年度日本水産学会秋季大会でgbdrawをお披露目しました。こちらが学会で発表したポスターです。 gbdrawは、ブラウザ上で環状・直鎖ゲノムを描画できるウェブアプリ (ローカルCUI版あり) です。論文や発表の図作成にぜひご活用ください。 gbdraw.streamlit.app github.com/satoshikawat...

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 09/09/2025

Released gbdraw v0.5.1! 🚀 I’ve completely revamped GC content/skew calculations and label processing, resulting in a dramatic speed boost. Install via Bioconda, or try it on the web app! github.com/satoshikawat...

github.com

GitHub - satoshikawato/gbdraw: A genome diagram generator for microbes and organelles

A genome diagram generator for microbes and organelles - satoshikawato/gbdraw

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