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/...

This is a feature I use a lot to help focus in on the parts of an alignment that are most relevant to my question. Incredibly helpful when combined with tree calculations to find the most interesting parts of huge sequence sets!

Jalview@jalview.bsky.social · 2w ago

🎩 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...

📬 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...

Another neat feature in Jalview that helps working with large alignments.

Jalview@jalview.bsky.social · last mo.

✂️ 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...

💾 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...

⚽ 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...

🏊🏼‍♂️ 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...

I’m really happy to see the Slivka preprint available. Take a look and try Slivka at www.compbio.dundee.ac.uk/slivka/.

Access services for multiple sequence alignment, structure predictions, disorder analysis, and conservation scoring provided by the DRSASP.

compbio.dundee.ac.uk

Jalview@jalview.bsky.social · 2mo ago

🗞️ 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.

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...

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

Protein secondary structure prediction by AlphaFold and Jpred combined in Jalview. Enjoy!

Jalview@jalview.bsky.social · 3mo ago

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...

Structural domain analysis it alphafold and Jalview

Jalview@jalview.bsky.social · 3mo ago

💊 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?...

🧮 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.

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...

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...

It’s blossom time of year again in sunny Dundee Scotland UK!

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...

💡AlphaFold's pLDDT scores can be visualised in Jalview as annotation tracks at the bottom - useful when comparing regions of high confidence across predicted protein structures in alignments. ▶️ For a guided tour of AlphaFold metrics in Jalview, watch: www.youtube.com/watch?v=WVCM...

With thanks to @wellcometrust.bsky.social @pdbeurope.bsky.social @ebi.embl.org @bartongrp.bsky.social @gjbarton.bsky.social @foreveremain.bsky.social and @stuartmac44.bsky.social

➡️ Watch our training video to find out more about structure discovery in Jalview: www.youtube.com/watch?v=ZBDZ...

Using 3D Beacons to access AlphaFold, Protein Data Bank and more in Jalview

YouTube video by Jalview & Dundee Resource Online Training

youtube.com

🔎 Browse extensive libraries of protein structures in Jalview using the 3D Beacons Network. Once imported, these can be colored, superimposed and viewed in 3D in conjunction with alignments. 👓 Synced views provide precision and clarity, allowing you to hone in on regions of importance.

I was very sad to hear this morning that Phil Bourne had passed away on 8th March. I've known Phil for many years but we had a great collaboration in the early days of the RCSB-PDB when he led the San Diego part of the consortium and I was in charge of the European project at EMBL-EBI. RIP Phil.

Alfonso Valencia@alfonsovalencia.bsky.social · 5mo ago

Phil Bourne, a key influential figure of our time for his positive, creative and ambitious thinking ... and doing! I remember working with him in @iscb.bsky.social and also fighting (and loosing) on OA/PlosCB issues. Now, both are fussed in good memories of the time with him. Rest in peace.

The annual crocuses on campus at #dundee university #scotland photo!

🌍 Twelve months of hard work - endless possibilities for world science. Watch our video tribute to the Jalview community for making 2025 such an incredible year for all of us! (Sound on 🗣️) Thank you all ❤️

🎉 Happy #new #year to everyone! 📢 No better way to kickstart 2026 than by sharing our latest work, now available on #Open #Biology by @royalsociety.org. The title is "Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish ints interaction with the Ser/Thr kinase CK1α".

❄️Thank you so much to all our users and followers worldwide for making 2025 such a memorable year for us! Seasons greetings to all from the Jalview team all the way from wintry Scotland.❄️ We hope to see you in the new year! ❤️

I have to say how happy I am that at least one of the disasters due to Brexit has been undone! Erasmus was always an amazing way to bring talented students to my lab to gain experience, great to see it will be possible again in the future! www.bbc.co.uk/news/live/c4...

Erasmus live updates: Scheme to return for UK students from 2027

British students will be able to spend a year studying at EU universities without paying extra fees, and vice versa for European students.

bbc.co.uk

💡Beacon of hope! Did you know Jalview allows you to access thousands of experimental and predicted protein structures programmatically through the 3D Beacons network? 🔽Find out how on our YouTube channel: www.youtube.com/watch?v=ZBDZ...

One of those November sunsets at Dundee Scotland today 😀

Forecast suggests it will be windy through the night. Much worse over on the West Coast of course! Stay safe!

West End Weather at Dundee, Scotland, UK@dundeeweather.bsky.social · 11mo ago

Storm Amy getting the wind up this evening!