Satoshi Kawato 川戸智
@kawatosatoshi.bsky.social
Evolutionary genomics of aquatic pathogens; Assoc. Prof. at Tokyo University of Marine Science and Technology, Japan
https://researchmap.jp/satoshi_kawato?lang=en
https://researchmap.jp/satoshi_kawato?lang=en
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
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
November 24, 2025 at 2:06 PM
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
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
Reposted by Satoshi Kawato 川戸智
#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...
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...
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...
link.springer.com
November 7, 2025 at 1:42 PM
#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...
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...
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
November 4, 2025 at 1:43 PM
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
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
November 4, 2025 at 1:40 PM
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
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
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
October 30, 2025 at 3:01 PM
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
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
Reposted by Satoshi Kawato 川戸智
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
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
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...
rdcu.be
January 8, 2025 at 1:19 PM
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
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
🚀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
- 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
October 26, 2025 at 1:34 PM
🚀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
- 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
Reposted by Satoshi Kawato 川戸智
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
www.nature.com
October 17, 2025 at 9:54 AM
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
🚀 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
- 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
October 9, 2025 at 2:01 PM
🚀 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
- 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
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
- 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
September 29, 2025 at 8:25 AM
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
- 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
Reposted by Satoshi Kawato 川戸智
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
Thread 1/n
September 25, 2025 at 9:29 PM
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
Thread 1/n
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...
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...
September 25, 2025 at 1:48 PM
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...
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...
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...
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...
September 9, 2025 at 1:40 AM
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...
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...
Draw the largest bacterial genome in 10 seconds.
Try out: gbdraw.streamlit.app
Try out: gbdraw.streamlit.app
September 8, 2025 at 7:58 AM
Draw the largest bacterial genome in 10 seconds.
Try out: gbdraw.streamlit.app
Try out: gbdraw.streamlit.app
Just released gbdraw v0.5.0! 🚀
- Support for GFF3+FASTA format input
- New label whitelist feature
- Local GUI version (optional; requires extra installation of Streamlit)
Please try our web app version until the Bioconda release is complete.
Check it out! gbdraw.streamlit.app
- Support for GFF3+FASTA format input
- New label whitelist feature
- Local GUI version (optional; requires extra installation of Streamlit)
Please try our web app version until the Bioconda release is complete.
Check it out! gbdraw.streamlit.app
September 1, 2025 at 3:00 PM
Just released gbdraw v0.5.0! 🚀
- Support for GFF3+FASTA format input
- New label whitelist feature
- Local GUI version (optional; requires extra installation of Streamlit)
Please try our web app version until the Bioconda release is complete.
Check it out! gbdraw.streamlit.app
- Support for GFF3+FASTA format input
- New label whitelist feature
- Local GUI version (optional; requires extra installation of Streamlit)
Please try our web app version until the Bioconda release is complete.
Check it out! gbdraw.streamlit.app
gbdraw v0.4.0 released!
- Label blacklist
- Custom label qualifiers
- Adjustable label arcs & font size
- Configurable axis color & width
Install with mamba or try online: gbdraw.streamlit.app
- Label blacklist
- Custom label qualifiers
- Adjustable label arcs & font size
- Configurable axis color & width
Install with mamba or try online: gbdraw.streamlit.app
August 9, 2025 at 5:48 AM
gbdraw v0.4.0 released!
- Label blacklist
- Custom label qualifiers
- Adjustable label arcs & font size
- Configurable axis color & width
Install with mamba or try online: gbdraw.streamlit.app
- Label blacklist
- Custom label qualifiers
- Adjustable label arcs & font size
- Configurable axis color & width
Install with mamba or try online: gbdraw.streamlit.app
I’ve improved the label rendering features in the gbdraw web app:
- selectively hide labels via a blacklist
- qualifier display priority customization
- adjustable label arcs
These updates make it easier to visualize larger genomes without layout issues.
gbdraw.streamlit.app
- selectively hide labels via a blacklist
- qualifier display priority customization
- adjustable label arcs
These updates make it easier to visualize larger genomes without layout issues.
gbdraw.streamlit.app
August 6, 2025 at 2:19 AM
I’ve improved the label rendering features in the gbdraw web app:
- selectively hide labels via a blacklist
- qualifier display priority customization
- adjustable label arcs
These updates make it easier to visualize larger genomes without layout issues.
gbdraw.streamlit.app
- selectively hide labels via a blacklist
- qualifier display priority customization
- adjustable label arcs
These updates make it easier to visualize larger genomes without layout issues.
gbdraw.streamlit.app
I’ve updated the web app for the genome visualization tool 𝙜𝙗𝙙𝙧𝙖𝙬!
- You can now place labels on the inner edge of circular genomes.
- Edit the color palette directly within the app.
👉Try it out: gbdraw.streamlit.app
- You can now place labels on the inner edge of circular genomes.
- Edit the color palette directly within the app.
👉Try it out: gbdraw.streamlit.app
July 23, 2025 at 2:27 PM
I’ve updated the web app for the genome visualization tool 𝙜𝙗𝙙𝙧𝙖𝙬!
- You can now place labels on the inner edge of circular genomes.
- Edit the color palette directly within the app.
👉Try it out: gbdraw.streamlit.app
- You can now place labels on the inner edge of circular genomes.
- Edit the color palette directly within the app.
👉Try it out: gbdraw.streamlit.app
The genome visualization tool gbdraw is now available as a Streamlit web app. Try it out:
gbdraw.streamlit.app
gbdraw.streamlit.app
July 17, 2025 at 9:34 AM
The genome visualization tool gbdraw is now available as a Streamlit web app. Try it out:
gbdraw.streamlit.app
gbdraw.streamlit.app
Built a web app to visualize BLASTN/TBLASTX XML results as SVG dotplots. Try it out:
blast2dotplot.streamlit.app
blast2dotplot.streamlit.app
July 16, 2025 at 9:35 AM
Built a web app to visualize BLASTN/TBLASTX XML results as SVG dotplots. Try it out:
blast2dotplot.streamlit.app
blast2dotplot.streamlit.app
Made a Streamlit web app to plot GC skew in microbial genomes. Check it out:
skewplot.streamlit.app
skewplot.streamlit.app
July 13, 2025 at 10:43 AM
Made a Streamlit web app to plot GC skew in microbial genomes. Check it out:
skewplot.streamlit.app
skewplot.streamlit.app
Made a Streamlit web app for ORF prediction. Check it out:
orfind.streamlit.app
orfind.streamlit.app
July 13, 2025 at 10:43 AM
Made a Streamlit web app for ORF prediction. Check it out:
orfind.streamlit.app
orfind.streamlit.app
gbdraw v0.2.0 released — now shipping with 55 color palettes!
Google Colab version also available:
github.com/satoshikawat...
Google Colab version also available:
github.com/satoshikawat...
May 26, 2025 at 2:04 PM
gbdraw v0.2.0 released — now shipping with 55 color palettes!
Google Colab version also available:
github.com/satoshikawat...
Google Colab version also available:
github.com/satoshikawat...
Just released: gbdraw, a lightweight genome diagram generator.
Visualize annotated genomes with a single command.
github.com/satoshikawat...
Visualize annotated genomes with a single command.
github.com/satoshikawat...
May 16, 2025 at 5:58 AM
Just released: gbdraw, a lightweight genome diagram generator.
Visualize annotated genomes with a single command.
github.com/satoshikawat...
Visualize annotated genomes with a single command.
github.com/satoshikawat...
Although still partially implemented, the genome visualization program gbdraw is now available for trial use on Colab Notebook.
colab.research.google.com/github/satos...
colab.research.google.com/github/satos...
May 8, 2025 at 12:27 PM
Although still partially implemented, the genome visualization program gbdraw is now available for trial use on Colab Notebook.
colab.research.google.com/github/satos...
colab.research.google.com/github/satos...