Jalview

Customise Jalview's sequence ID tooltip by selecting View ➡️ Sequence ID Tooltip. Database references from @ebi.embl.org UniProt, EMBLCDS and ENSEMBL can then be shown in the tooltip if required — and accessed from Jalview using the 'Link' option. 🧮 Download Jalview: www.jalview.org/download/

💭 Do JPred’s sequence-based secondary structure predictions agree with AlphaFold’s 3D structure-based ones? Find out with Jalview! Learn how to compare outputs to explore: ✅ Locations of shared helices and sheets ✅ Regions of prediction confidence ▶️ Watch: www.youtube.com/watch?v=x7SH...

📂 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/

👓 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...

📝 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

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

📣 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...

✂️ 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...

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/...

🎩 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...

📺 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.

And... 🚂 A bonus 1 hour Jalview whistle stop tour: www.youtube.com/watch?v=RTCk...

📺 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.

📺 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...

📬 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...

✂️ 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...

🗞️ 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...

⚙️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.

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...

💊 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.

📺 Learn more: www.youtube.com/watch?v=-5kg...

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...