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Jalview @jalview.bsky.social · 12d

🌍 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! ✨

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Jalview @jalview.bsky.social · 20d

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

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Jalview @jalview.bsky.social · 20d

🕵️‍♂️ 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...

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Jalview @jalview.bsky.social · 27d

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

www.compbio.dundee.ac.uk

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Jalview @jalview.bsky.social · 27d

🗣️ 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...

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Jalview @jalview.bsky.social · Sep 6

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

Jalview @jalview.bsky.social · Sep 5

📥 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!

https://www.jalview.org/download/

jalview.org

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Jalview @jalview.bsky.social · Sep 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.

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.

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Jalview @jalview.bsky.social · Aug 7

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

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Jalview @jalview.bsky.social · Aug 7

✅ 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...

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.

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Jalview @jalview.bsky.social · Aug 6

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

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Jalview @jalview.bsky.social · Aug 6

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

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Jalview @jalview.bsky.social · Aug 1

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.

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Jalview @jalview.bsky.social · Aug 1

🚀 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...

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Jalview @jalview.bsky.social · Jul 17

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.

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Jalview @jalview.bsky.social · Jul 17

📣 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...

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.

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Jalview @jalview.bsky.social · Jul 2

🖼️ 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...

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

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Jalview @jalview.bsky.social · Jun 3

@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

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Jalview @jalview.bsky.social · Jun 3

🌼 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!

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

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Jalview @jalview.bsky.social · Jun 3

💡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...

Alignment algorithms available from within Jalview.

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Jalview @jalview.bsky.social · May 15

🚀 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...

Using 3D Beacons to access AlphaFoldDB, PDB and more in Jalview

YouTube video by Jalview & Dundee Resource Online Training

www.youtube.com

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Jalview @jalview.bsky.social · May 7

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

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.

www.jalview.org

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Jalview @jalview.bsky.social · May 7

👀 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...

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Jalview @jalview.bsky.social · Apr 23

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

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Jalview @jalview.bsky.social · Apr 23

💡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...

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