Jalview

🌍 This week, we had the pleasure of providing training to the new cohort of life sciences postgraduate students at the University of Dundee. An array of topics were covered from the basics of multiple sequence alignment to AlphaFold structure quality in Jalview.

All the best for the future! ✨

With thanks to
@wellcometrust.bsky.social, @gjbarton.bsky.social, @foreveremain.bsky.social, @stuartmac44.bsky.social and
@khadijasvoice.bsky.social.

🕵️‍♂️ Attention sequence sleuths! 🕵️‍♀️

🔎 Did you know you can detect similar sequences of protein, DNA and RNA in Jalview using PCA? This makes it easier for conserved regions, including functional subgroups, to be identified.

▶️ Watch our training video to find out how: www.youtube.com/watch?v=KdCx...

More information about the JPred server, including help resources, can be found here: www.compbio.dundee.ac.uk/jpred4/help....

🗣️ Did someone say secondary structure?

In this training video, Suzanne demonstrates how JPred4 can be used to perform secondary structure prediction jobs on single protein sequences.

Watch here: www.youtube.com/watch?v=xwTk...

With thanks to @wellcometrust.bsky.social @gjbarton.bsky.social @foreveremain.bsky.social @stuartmac44.bsky.social and @khadijasvoice.bsky.social

📥 Ready to upgrade?
Download Jalview 2.11.5 now: jalview.org/download

📌 Note: This is the last minor release in the 2.11 series.
All future features and fixes are heading into Jalview 2.12 - stay tuned!

The new secondary structure annotation tree showcasing all protein secondary structure providers available for sequences in a sample ferredoxin alignment in Jalview 2.11.5.

🚀 Jalview 2.11.5 is here!

New features include:
✅ Tree visualisation for enhanced protein secondary structure analysis
✅ Consensus colouring for alignments and subgroups
✅ Improved command line options for 3D structure visualisation

Plus, key bug fixes and performance improvements.

@wellcometrust.bsky.social @gjbarton.bsky.social @foreveremain.bsky.social @stuartmac44.bsky.social @khadijasvoice.bsky.social @pdbeurope.bsky.social @ebi.embl.org

Jalview CDS-protein split-screen view showing gene and protein products for homogentisate 1,2 dixoygenase (ENSEMBL ID: ENSG00000113924) in 2D and 3D with VCF variants highlighted in red.

✅ Import genomics VCF files and analyse data like a pro!

Watch Mungo as he outlines how genetic variant data can be imported into and visualised in Jalview using our signature CDS-protein split-screen feature.

Link here: www.youtube.com/watch?v=n_lR...

Thanks, guys! Do follow us here for more updates on new features and releases! ✨

So pleased it worked out for you, Joachim! Follow us here for more updates on new features and releases ✨

With thanks to @wellcometrust.bsky.social @gjbarton.bsky.social @bartongrp.bsky.social
@foreveremain.bsky.social @khadijasvoice.bsky.social
@stuartmac44.bsky.social bsky.social
@javierutges.bsky.social and the wider Barton research group.

🚀 Our latest AlphaFold video is out! Find out how you can discover hidden domains in your AlphaFold models using Jalview's PAE-focused cluster analysis.

▶️ Watch the full video here: www.youtube.com/watch?v=pQC8...

With thanks to @wellcometrust.bsky.social @gjbarton.bsky.social, @bartongrp.bsky.social, @foreveremain.bsky.social, @khadijasvoice.bsky.social, @stuartmac44.bsky.social, @javierutges.bsky.social and the rest of the Barton research group.

A protein sequence alignment in Jalview with reference annotation tracks consisting of the pLDDT score, secondary structure and PAE dowloaded for each sequence where data is available from AlphaFoldDB.

📣 Working with AlphaFold's PAE? The latest instalment in our 'Protein Model Quality' series may be of help! Find out how you can visualise the metric with your alignments and 3D structures in Jalview.

▶️ Watch the new training video here: www.youtube.com/watch?v=jowU...

Multiple sequence alignment in Jalview synced with outputs featured in tree, PCA and 3D molecular graphics viewers.

🖼️ Did you know you can export high-quality images from Jalview?

Find out how coloured alignments, phylogenetic trees and PCA plots can be turned into vibrant publication-worthy figures - all with the click of a few buttons.

▶️ Watch our training video on the topic: www.youtube.com/watch?v=wSov...

@nanoporetech.com @minipcr.bsky.social @wellcometrust.bsky.social @gjbarton.bsky.social @bartongrp.bsky.social @khadijasvoice.bsky.social @malcolmacaulay.bsky.social @foreveremain.bsky.social @stuartmac44.bsky.social @javierutges.bsky.social

Jalview, Daffodil DNA and James Hutton Institute exhibition booths at the ASE 2025 Conference in Cupar, Scotland.

🌼 Jalview and The Daffodil DNA Project were at the 2025 Conference @associationscied.bsky.social this weekend with colleagues from James Hutton.

🧬Lots of chats with folks about all things bioinformatics, DNA sequencing, multiple sequence alignment and protein structure!

Alignment algorithms available from within Jalview.

💡Alignment aficionados! Ever wondered how to easily use your favourite alignment methods? ClustalO, TCoffee, MAFFT, MUSCLE and more can be accessed from Jalview to align protein, DNA and RNA sequences.

⏩ Refresh your insights with our instructional video: www.youtube.com/watch?v=Majc...

YouTube video by Jalview & Dundee Resource Online Training Using 3D Beacons to access AlphaFoldDB, PDB and more in Jalview

🚀 Structure alert: Discover protein models in Jalview using the 3D Beacons network. Browse thousands of experimental and predicted structures from Protein Data Bank, AlphaFold, SWISS Model and more with the click of a few buttons!

▶️ Watch our instructional video: www.youtube.com/watch?v=ZBDZ...

View Ensembl Features on Protein-CDS Alignments - Jalview Select File ⇒ Fetch Sequences and select ENSEMBL from the list of databases in the New Sequence Fetcher dialog box, enter the accession number ENSG00000113924 and click OK. Progress is indicated in the status bar at bottom of the window.

And here is a link to the training exercise: www.jalview.org/tutorial/exe...

👀 Visualise pathogenic variants in Jalview's protein-CDS split screen window as you map these onto your favourite 3D molecular viewer! We have PyMol, ChimeraX, UCSF Chimera and JMol available for your analyses.

Watch our 'Genome to Function' video to find out how: www.youtube.com/watch?v=e/6a...

With thanks to @wellcometrust.bsky.social @bartongrp.bsky.social @gjbarton.bsky.social @foreveremain.bsky.social @stuartmac44.bsky.social @javierutges.bsky.social @khadijasvoice.bsky.social

💡Protein lovers - a brand NEW video exploring AlphaFold's pLDDT score in Jalview is out! Find out how you can select, hide and colour your alignments using this 3D structure prediction confidence metric.

▶️ Watch the full video here: www.youtube.com/watch?v=WVCM...

✏️ And here: www.jalview.org/tutorial/exe...

✏️ Hands-on exercises can be found here: www.jalview.org/tutorial/exe...

YouTube video by Jalview & Dundee Resource Online Training 3D Molecular Structure Jmol and UCSF Chimera viewers in Jalview

✨ Watch the training video: www.youtube.com/watch?v=yRBL...
PyMol and ChimeraX are supported in Jalview in a similar way.

💡Calling all visualisation enthusiasts - did you know Jalview can help you bring your alignments to life in more ways than one?

Experience the beauty of molecular graphics with four 3D viewers - PyMol, UCSF Chimera, JMol and ChimeraX - all accessible from Jalview!

@wellcometrust.bsky.social @bartongrp.bsky.social @gjbarton.bsky.social @foreveremain.bsky.social @stuartmac44.bsky.social @javierutges.bsky.social @khadijasvoice.bsky.social