iiinova — where your digital self keeps evolving

Jalview @jalview.bsky.social · 25/09/2026

This week, we trained new University of Dundee research students exploring areas in 🧫 biology, 🪴plant sciences, 🧬bioinformatics, 🦷 dentistry & 🤰reproductive medicine. From sequence alignment & analysis to 3D structure discovery, we explored how Jalview can support their research. Happy Jalviewing!

Three female students using Jalview, with the PC of the nearest student showing the Jalview desktop with a multiple sequence alignment shaded using the turn propensity colour scheme developed using mathematical values computed by Peter Y. Chou and Gerald D. Fasman in the 1970s.

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Jalview @jalview.bsky.social · 18/09/2026

📂 Who says iPhones have all the folding fun? If your alignment is wider than your screen, try Jalview’s ‘Wrap’ feature! Fold long alignments neatly into your window — then add scales on the left, right or top to create polished figures for papers, seminars & tutorials. ⬇️ www.jalview.org/download/

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Jalview @jalview.bsky.social · 15/09/2026

👓 Visualising sequence alignments in 3D? Jalview enables multiple structures to be visualised with Chimera, ChimeraX, PyMOL and Jmol — helping scientists and educators bring biology to life. 📺 Explore the editor's functionality: www.youtube.com/watch?v=pbms... www.youtube.com/watch?v=yRBL...

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Jalview @jalview.bsky.social · 11/09/2026

Many other useful alignment characteristics can also be accessed. ⬇️ Download Jalview: www.jalview.org/download/

jalview.org

Download - Jalview

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Jalview @jalview.bsky.social · 11/09/2026

📝 Quick tip: You can find the number and length of sequences in your Jalview alignment from the 'View' menu! Select 'Alignment properties' and discover a wealth of information, including: 🧮 Total number of sequences 🧮 Minimum sequence length 🧮 Maximum sequence length 🧮 Average length

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Jalview @jalview.bsky.social · 07/09/2026

📣 Calling all sequence sleuths! 📣 Our latest training video investigates how colouring by conservation in Jalview can be used to deduce the locations of intermolecular interactions like salt bridges in a protein family. 📺: www.youtube.com/watch?v=1O34...

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Jalview @jalview.bsky.social · 20/08/2026

✂️ Editing sequence alignments in Jalview is flexible and reversible. Move sequences ↕️, create groups 👥, insert gaps ➖, using both mouse or keyboard. Edits can also be undone! 🎥 Learn how: www.youtube.com/watch?v=FXGI...

Keyboard with finger hovering over the section containing the up, down and left and right keys.

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Jalview @jalview.bsky.social · 05/08/2026

Batches of protein sequences can be submitted to the JPred server for protein secondary structure prediction, with the option to receive a copy of the results via email. 🔗 www.youtube.com/watch?v=yLga... 🔗 www.compbio.dundee.ac.uk/jpred/help.s... 📜 academic.oup.com/nar/article/...

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Jalview @jalview.bsky.social · 31/07/2026

🎩 Sequences can be hidden in Jalview, allowing specific subsets within the alignment to be focused on and analysed. Hiding sequences improves the readability of large MSAs and the presentation of results for publication. 🔗 www.youtube.com/watch?v=9s7W... 🔗 www.jalview.org/tutorial/exe...

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Jalview @jalview.bsky.social · 24/07/2026

📺 Determining alignment quality: www.youtube.com/watch?v=udWX... 📺 Predicting protein secondary structure: www.youtube.com/watch?v=RZ6c... 📺 Analysing protein sub-families: www.youtube.com/watch?v=so7Z...

youtube.com

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Jalview @jalview.bsky.social · 24/07/2026

📺 Finding protein structure files: www.youtube.com/watch?v=KC2_... 📺 Classifying protein structures: www.youtube.com/watch?v=mAei... 📺 Defining MSA: www.youtube.com/watch?v=9ZFj... 📺 Generating MSAs: www.youtube.com/watch?v=Ym9Z...

youtube.com

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Jalview @jalview.bsky.social · 24/07/2026

📺 Powering off your tech devices for the summer? Learning never stops! You can watch key bioinformatics lectures by Prof. Geoff Barton on the fundamentals of MSA analysis on your TV instead. Plus, a free 1 hour Jalview masterclass by Jalview Co-ordinator, Dr. Jim Procter. 🔗 Links in comments.

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Jalview @jalview.bsky.social · 23/07/2026

📬 Protein and nucleotide structures can be imported into Jalview, mapped on to MSA sequences and visualised in 3D. Our latest training video summarises some of the structure import options available to users. ▶️ Watch it here: www.youtube.com/watch?v=xFUu...

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Jalview @jalview.bsky.social · 16/07/2026

✂️ Sequence redundancy can create bias and slow down the analysis of alignments. With Jalview, you can quickly reduce redundancy by filtering sequences based on percentage identity. Just adjust the threshold slider to your chosen cutoff! Read more: www.jalview.org/tutorial/exe...

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Jalview @jalview.bsky.social · 10/07/2026

💾 Taking a break? Save your work in Jalview! Alignments, annotations, trees, structures, colours, views and more can be preserved in Jalview, enabling you to begin where you left off. ⬇️ Find out more. 🔗 www.youtube.com/watch?v=xT4g...

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Jalview @jalview.bsky.social · 01/07/2026

⚽ As football fever builds, there’s one competition where every nation is poised to win. 📺 Jalview’s YouTube channel has been watched 250,000+ times by scientists, students and bioinformaticians across 150+ countries. 🧬 Why not tune in too? ⬇️ Link below. 🔗 www.youtube.com/@jalviewtrai...

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Jalview @jalview.bsky.social · 23/06/2026

🏊🏼‍♂️ Dive into molecular structures this summer with Jalview’s integrated 3D viewers. Visualize thousands of protein, DNA and RNA structures with PyMOL, Chimera, ChimeraX and Jmol — whether you're an experienced bioinformatician or just getting started! ▶️ Learn more: www.youtube.com/watch?v=pbms...

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Jalview @jalview.bsky.social · 18/06/2026

🗞️ New preprint: Slivka & Slivka-bio — a lightweight framework for turning command-line tools into web services, developed by Jalview, the Dundee Resource and Genentech. 📜 www.biorxiv.org/content/10.6... ⚡Slivka-bio is set to replace JABAWS in a future release.

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Jalview @jalview.bsky.social · 10/06/2026

Explore the adverse effects of genetic mutations in 2D and 3D views by loading the coding DNA of protein sequences. 1️⃣ Jalview's protein-CDS view: www.youtube.com/watch?v=qFMJ... 2️⃣ Feature mapping: www.youtube.com/watch?v=eK6a... 3️⃣ Genomics file imports: www.youtube.com/watch?v=n_lR...

An alignment of ferredoxin proteins in Jalview with associated coding DNA sequences shown above in the split-screen view. Binding sites imported from UniProt are highlighted in pink in all views, including the associated AlphaFold structure displayed on the right in ChimeraX.

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Jalview @jalview.bsky.social · 27/05/2026

🔗 JABAWS: hub.docker.com/r/drsasp/jab... 🔗 Jalview Develop: www.jalview.org/development/... 🔗 SLIVKA: www.compbio.dundee.ac.uk/slivka/#cta-...

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Jalview @jalview.bsky.social · 27/05/2026

⚙️Large alignments can be tackled in Jalview by running alignment services using Slivka in Jalview 2.12 (now available via Jalview Develop). Downloading a local copy of JABAWS is another option. ⬇️ See below for links to both.

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Jalview @jalview.bsky.social · 21/05/2026

Protein secondary structure can be inferred using a number of machine learning methods. In our latest training video, we explore how two such methods — AlphaFold and JPred — can be accessed from Jalview to compare and contrast results. ▶️ Watch it here: www.youtube.com/watch?v=x7SH...

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Jalview @jalview.bsky.social · 13/05/2026

💊 Finding druggable protein domains is hard—but AlphaFold's PAE data can help. Jalview lets you import this into alignments, so it can be clustered to understand protein structure better. ➡️ PAE import: youtu.be/jowUEG47F-Q?... ➡️ Domain detection: youtu.be/pQC8LTDCbug?...

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Jalview @jalview.bsky.social · 06/05/2026

🧮 Are you making the most of Jalview’s annotation rows? These visual layers add context for interpreting biological structure & function: conservation, alignment quality, consensus, secondary structure, AlphaFold's pLDDT & PAE. ➡️ Group/user-specific annotations can also be created.

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Jalview @jalview.bsky.social · 01/05/2026

Boost your workflow with Jalview’s 'Find' function! ✅ Locate motifs sequentially or en masse ✅ Designate hits as new features ✅ Copy to other alignments ✅ Visualize rapidly using the 'Overview Window' ⏰ Save time and see the big picture. 📖 Read more: www.jalview.org/help/html/fe...

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Jalview @jalview.bsky.social · 24/04/2026

JPred predicts protein secondary structure from multiple sequence alignments—and you can access it directly from Jalview. Supported file formats include: ✅ MSF ✅ FASTA ✅ BLC Add your email to get notified when your job finishes 🪄 ▶️ Learn more in our training video: www.youtube.com/watch?v=EW6b...

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Jalview @jalview.bsky.social · 17/04/2026

Did you know Jalview can bring your alignments to life in 3D? Experience the beauty of molecular graphics with PyMol, UCSF Chimera, ChimeraX and JMol in the editor. ▶️ Watch our NEW training video for more insights: www.youtube.com/watch?v=pbms...

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