Jalview Home Page on Jalview

How do I run Jalview?

Mon, 02 Jul 2012 12:06:25 +0100

You need a computer that can run at least Java 1.7 to use the full Jalview application(unfortunately this excludes users with older Macs - sorry). If java is installed, then the ‘Launch Jalview Desktop’ link at the top should work (if your browser asks you to save the application-x-jnlp file or choose an application to run it with, look for ‘Java Web Start’, or locate your java installation directory and look for the javaws binary). You can also go to the Install Anywhere Web Installer download area area to get an installer for your platform.

How do I edit sequences in Jalview?

Mon, 02 Jul 2012 12:38:13 +0100

Use the Mouse

Use the cursor keys

Edit Selected Region Only

Press F2 to enter Keyboard Mode

Can I install Jalview on a server?

Mon, 02 Jul 2012 13:01:54 +0100

Yes! Just remember to include the --headless flag on the command line (this is the default if your command is going to output a sequence or image file).

For example:

jalview --headless --open ...

The latest version of Jalview should run fine on a server without a graphics environment, but some operations may fail. If you encounter problems, submit a bug report.

How do I get the consensus sequence for an alignment?

Mon, 02 Jul 2012 12:49:28 +0100

Right-click on the ‘Consensus’ label for the consensus annotation track, and select “Copy consensus sequence”.

How do I increase the memory available to Jalview?

Mon, 02 Jul 2012 13:00:34 +0100

Full instructions for different operating systems and installations are here. If yours isn’t listed, drop us a line at the help address.

Important Messages

Mon, 25 Mar 2024 00:00:00 +0000

tl;dr

Copy one of the message files in content/important_messages/ and change the publishDate, expiryDate, startDate, title and importance values. Also change the content to the message you want to appear!

If you want a red box, give an importance value of 100 or more. If you want a grey box, give an importance value of between 0 and 99. If there is more than one message box, the order is from highest importance value to lowest.

Adding an album using Lightbox2

Thu, 31 Mar 2022 00:00:00 +0000

tl;dr

Use the following to make a lightbox album with one image on the web page and several images, with different captions, displayed in the album when you click on the visible image.

{{<lightbox src="a_busy_picture.jpg" title="Busy diagram with lots going on" lightbox="diagram" class="small">}}General description{{</lightbox>}}
{{<lightbox src="some_detail_of_this_bit.jpg" title="Here is some detail about this bit" lightbox="diagram" class="small" hidden=true >}}{{</lightbox>}}
{{<lightbox src="some_detail_of_that_bit.jpg" title="Here is some detail about that bit" lightbox="diagram" class="small" hidden=true >}}{{</lightbox>}}
{{<lightbox src="some_more_detail_of_that_bit.jpg" title="Here is some more detail about that bit" lightbox="diagram" class="small" hidden=true >}}{{</lightbox>}}

Partial and shortcode

A partial and associated shortcode have been created to easily make use of Lightbox2.

Embedding Local Video Files and Screen Captures

Thu, 31 Mar 2022 00:00:00 +0000

tl;dr

Convert videos to mp4 (H.264, AAC encodings) and webm (VP9, OPUS encodings) and make a poster image

cd themes/layouts/static/videos
../../../../scripts/convert_videos.sh /path/to/my/video_file_basename.mov
ffmpeg -ss 00:00:01 -i /path/to/my/video_file_basename.mov -frames:v 1 poster/vide_file_basename.png

then use this shortcode in your markdown:

{{<embed-video alt="My caption" src="video_file_basename">}}

Partial and shortcode

Two partials and shortcodes have been made to easily use Video.js for displaying screen captures or general video embedding.

When you use one of the shortcodes embed-video or screen-capture, the page should automatically pull in the minimised Javascript and CSS required (this is performed in head-meta.html which, when appropriate, calls the partial video-js-init.html which in turn includes the required JS and CSS files).

Copy to Clipboard and command blocks

Wed, 30 Mar 2022 00:00:00 +0000

tl;dr

You’re probably better off reading all of this page. The section on copy-to-clipboard-start, copy-to-clipboard-id is the most useful.

Partials and shortcodes

The Copy-to-clipboard functionality in the website uses the There are several ways to include a copy-to-clipboard clipboard.js javascript which is lightweight. As such there’s a bit of styling and icons added on top of that.

As there are a couple of different ways to use the copy-to-clipboard functionality there are a few different partials/shortcodes to have get to grips with.

Creating partials and shortcodes (a recommendation)

Wed, 30 Mar 2022 00:00:00 +0000

tl;dr

Make a partial that expects to receive a dictionary as the argument. The dictionary should contain (dict "page" $.Page "site" $.Site) as a minimum if indeed the partial uses those objects. You can then refer to the $.Page using .page in the partial.

Make a shortcode with the same filename that contains

{{- partial (printf "%s.html" .Name) (merge .Params (dict "page" $.Page "site" $.Site)) -}}

Displaying something different for different platforms

Wed, 30 Mar 2022 00:00:00 +0000

tl;dr

Use the following classes in your HTML and the following shortcode to display something different for different platforms:

You are viewing this in
<span class="os_detect os_detect_windows os_detect_hidden">Windoows</span>
<span class="os_detect os_detect_linux os_detect_hidden">Linooks</span>
<span class="os_detect os_detect_macos os_detect_hidden">macOOS</span>
<span class="os_detect os_detect_unix os_detect_hidden">some oOther Unix (other than Linux)</span>
<span class="os_detect os_detect_not_all">... umm, I dunno</span>
.

Or more briefly you are viewing this in <span class="os_detect os_detect_any os_detect_osName">... I still don't know</span>
.
{{% os-detect-hide %}}

To produce:

You are viewing this in Windoows Linooks macOOS some oOther Unix (other than Linux) … umm, I dunno .

Adding Images and Video

Fri, 07 Dec 2018 14:21:35 +0000

Custom image shortcodes and an example of Hugo’s built-in Youtube video shortcode.

Where shortcodes are built-in links to Hugo documentation are provided.

Large images (wider than 320px)

The img-auto-src shortcode will generate derivative images and HTML code for the HTML image srcset attribute. The output HTML allows responsive lazy-loaded images.

{{<
  img-auto-src
  src="example.jpg"
  link="/an-optional-link/"
  alt="A description of the image"
  class="optional-css-class another-class"
  loadingAttribute="optional loading attribute"
 >}}

Only the src and alt attributes are required, all others are optional.

F2 key does not toggle Cursor mode on my Mac?

Mon, 02 Jul 2012 12:50:03 +0100

You may be using a keyboard which has visual / audio settings mapped onto the Function keys. You must press the “Fn” key, together with F2 key to toggle Cursor Mode.

Can I run Jalview from the command line?

Mon, 02 Jul 2012 12:52:51 +0100

Yes. The Jalview Desktop has a number of command line options, and recent versions of the Jalview Desktop application come with a command line tool ‘jalview’ that allows you to call it from the command line.

Open a command prompt or terminal and try:


jalview --help

This should list the current set of arguments Jalview supports. The online documentation also includes a list of jalview command line parameters

Note: This FAQ has been updated - we no longer recommend the -Djava.ext.dirs=lib argument since it prevents Jalview from accessing some web services, and will be disabled in future versions of Java.

Does Jalview work with nucleotide sequences and alignments?

Mon, 02 Jul 2012 12:51:37 +0100

Yes. All versions of Jalview after 2.8 (released Nov 2012) include special support for nucleic acid sequences, and employ a substitution matrix that copes with both RNA and DNA symbols to calculate trees and principal component analysis plots from alignments. Nucleotide base pair patterns provided as WUSS or VIENNA dot-bracket annotation can also be visualised, and used to calculate base-pair consensus score and sequence logos. Version 2.8 of the Jalview Desktop also includedVARNA for interactive exploration of 2D RNA structure. For the latest information about nucleic acid support, see the nucleic acid section of Jalview’s help pages.

Colour Palette

Fri, 07 Dec 2018 14:21:35 +0000

Derived from logo. Defined in 'colors.css'.

white

text-black

black

grey-background

grey-lighter

grey

grey-darker

blue-lighter

blue

blue-darker

orange-lighter

orange

orange-darker

purple-lighter

purple

purple-darker

green-background

green-lighter

green

green-darker

sky-lighter

sky

sky-darker

Something that normally works in Jalview has stopped working! What should I do?

Mon, 02 Jul 2012 13:01:09 +0100

One of the commonest causes of ‘strange behaviour’ that our users have reported seems to be Jalview running out of memory. Memory errors can cause some operations to fail silently - with no warning, annotations may disappear from the alignment window, and web service calculations (apparently) never finish.

You should be able to see something in the error log - see the instructions for bug reporting on how to view this. If you do see ‘Out of memory’ or ‘Cannot allocate stack’ or ‘HeapAllocationError’ type messages, then you might be able to fix it by increasing the memory available to jalview.

How do I report a bug in Jalview?

Mon, 02 Jul 2012 13:01:31 +0100

Firstly, see if you can reproduce the bug. Check Jalview’s memory settings (Desktop->Tools->Show Memory usage) to make sure you have at least 50% memory free when testing this. If not, the problem might be because you ran out of memory when using Jalview.

Then, follow the instructions below to gather essential information regarding the bug:

The Jalview desktop includes a Java Console - this is disabled by default, but if you enable it from the Desktop->Tools->Show Java Console menu item, a window will open that will contain the version of jalview and information about your operating system.
- The jalview java console can slow down some operations. If it takes too long to reproduce your bug with the console open, then close it and try another way below:
If you installed Jalview using Java Webstart, locate and start the program “javaws” or “javaws.exe” on your system. Then click the “Edit” menu, select “Preferences” then click the “Advanced” tab. Make sure you check the “Java Console” option to “Show Console”, then click “OK” and restart Jalview. A Java console will be shown when Jalview starts up, and information about any problems should be output to the console window.
If you installed Jalview with InstallAnywhere, you will find a text file in the directory in which you installed Jalview called “output.txt” Include this file with any bug report you have.

Prepare the input data and a description of how the bug is reproduced

The old Jalview had font size and page orientation settings for its Postscript output. Where have they gone?

Mon, 02 Jul 2012 12:59:59 +0100

Jalview now exports images and graphics using the same settings as the alignment display window. Just set the font and font size, and the layout style (normal or wrapped) using the View menu.

If you do want to specify portrait or landscape, you could use the File->Print dialog box, and redirect the output to a file.

A Jalview file I created in an earlier version of Jalview no longer loads.

Mon, 02 Jul 2012 13:04:30 +0100

We have tried to ensure that all files created in earlier versions of Jalview can be read in by later versions. If you have a Jalview format file which no longer loads, please let us know by emailing the file to us. It is possible other people are having the same problem!

Jalview's Installer won't run on my Mac

Fri, 01 Nov 2013 14:38:48 +0000

Here are some symptoms we’ve observed when Jalview has failed to launch via webstart, or the Jalview installAnywhere could not be run.

In all cases, the Web start file (jnlp) and the Installer downloaded and unpacked successfully.

Running the installer/jnlp file opens a “This program cannot be run because it comes from an unidentified developer”.
- For some reason, your Mac has not recognised our Apple Developer Signature (if you are running Jalview 2.8.1,please tell us about this!)
- Follow step 1, below - select the ‘Run anyway option’
Running the installer opens a “This fileis damaged and should be moved to the trash”
- In this case, your Mac thinks someone has tampered with the installation program, although actually, what has happened is that you’ve probably just downloaded a new version of Jalview.
- You need to followstep 2 below - temporarily disable the security check
Installer downloads but double clicking it does nothing.
- This usually means that there is something wrong with your Java installation.
1. Control-click the install-jalview package and select the “Open Package Contents” option.
2. Double click through the directories:Contents,MacOS
3. Double click on ‘install-jalview’ (or ‘install’, for older Jalviews)- this will open up a terminal window with some commands that executethe installer program.
- If the installer still doesn’t launch, send us an email via jalview-discuss@jalview.org to let us know what the message is.

Changing the gatekeeper settings

First, open your system settings panel, and go to the security and privacy section:

My application doesn't like the "/start-end" sequence suffix in files saved by Jalview

Mon, 02 Jul 2012 13:05:11 +0100

In the application, open the preferences dialog window (Tools -> Preferences) Open the tab labelled “Output” and then select which file formats to which you do not wish to append “/start-end”

Can't see databases in Database Chooser after selecting Fetch Sequences...!

Sat, 08 Oct 2016 09:32:22 +0100

Note - this is a bug affecting an old version of Jalview - if you experience this problem with the latest version please let us know.

If you are running Jalview 2.10.0 under Ubuntu or some other (possibly GTK based) Linux desktop, you may find that after opening the Sequence Fetcher, you are presented with a dialog box just showing ‘OK’ and ‘Cancel’ buttons, but nothing much else. The empty panel is due to an underlying problem with Java, but you can still choose from the list of databases with the keyboard !

Fuzzy fonts in the alignment view on OSX Mojave (10.14.x)

Mon, 08 Oct 2018 10:29:41 +0100

On OSX Mojave, you may notice that sequences and IDs in the Jalview alignment window are hard to read. To fix this, first:

Save your work and shut down Jalview
Open a Terminal window (use spotlight or the Launcher and type ‘Terminal’ to locate the Terminal App), and type:

defaults write -g CGFontRenderingFontSmoothingDisabled -bool NO

Start Jalview again and load an alignment to check that the fonts are now legible.

Thanks to Marcin for reporting this issue and testing the workaround via issues.jalview.org/browse/JAL-3134

Jalview's menus and fonts are too small on my Windows machine !

Tue, 26 Feb 2019 18:25:16 +0000

When Jalview is run on Windows machines with high resolution displays (e.g. 4K, retina, etc) resolution screens, you might find that all the menus, window titles, and alignment data are really tiny. That’s because on high-resolution displays, all the windows and fonts have to be magnified so that you can read them, and the fix is to ask Windows to do the same for the Jalview application.

Instructions on how to do this can be found in several places on the ’net.

Jalview has encountered an error during launch

Thu, 20 Jun 2019 10:00:56 +0100

If you’ve been redirected to this FAQ then it probably means that the Jalview Native application has encountered an error whilst trying to start. Here are some tips for various problems:

Problems on Windows:

If your installation of Jalview goes fine, but double clicking on the Jalview icon does not produce any error message, window or any other activity (other than the spinning blue circle) this might be caused by a space character in Jalview’s installation folder. To fix this:

Jalview's Menus and Fonts are too small on my Linux machine

Thu, 30 Apr 2020 16:59:23 +0100

If you are running Jalview in Linux with a HiDPI or 4K monitor then the font size and menus are likely to be too small to be practical.

UPDATE: Jalview 2.11.1.1 and above should automatically detect a Linux HiDPI display, and scale the application appropriately if you are using the Java 11 version. You can download a newer installer from https://www.jalview.org/getdown/release/install4j/11/jalview-2_11_1_1-linux_x64-java_11.sh (coming soon!).

Jalview doesn't install/always crashes on startup in Windows when I have non-ASCII characters in my username.

Thu, 21 Nov 2024 00:00:00 +0000

There is a long-running bug in Java, mainly affecting Windows, that fails to read command line arguments with non-ASCII characters correctly.

For Jalview versions < 2.11.5.0 you will have to install Jalview in a location that doesn’t include your username, such as C:\Program Files\Jalview. This unfortunately requires Administrator privileges and will need all automatic updates to be turned off (only available in 2.11.4.0). For earlier versions you could install Jalview in C:\Temp\Jalview although this folder often gets emptied, so you may need to reinstall.

Fonts look incorrectly sized in Ubuntu Linux

Mon, 04 May 2020 20:04:05 +0100

If you are running Jalview in Ubuntu Linux and think that fonts look incorrectly sized, like the following screenshot,

you can turn off the Ubuntu system default (for Java swing applications) Gtk “Look and Feel” by running Jalview with the environment variable JAVA_TOOL_OPTIONS by running Jalview with the following command:

JAVA_TOOL_OPTIONS="-Dswing.systemlaf=javax.swing.plaf.metal.MetalLookAndFeel" ~/opt/jalview/jalview

To make this option always apply you can edit the file

~/opt/jalview/jalview

(or the script “jalview” in the directory you installed Jalview into) and add the following to the as the second or third line:

How do I set web proxy settings for Jalview's auto-updater and web services?

Thu, 09 Jul 2020 20:33:52 +0100

Jalview uses a launcher (called getdown, see https://github.com/threerings/getdown) that runs an auto-updater for Jalview and verifies Jalview files by checking the Jalview web site. Whilst the launcher checks for existing system proxy settings, sometimes it does not find those settings. In this case it may pop up a window asking for proxy settings. If this does not happen, and proxy settings are required, you can create a file called

proxy.txt

that should contain your proxy host and port like this:

Jalview failed to launch, displaying an error saying it was "unable to download the necessary files"

Thu, 03 Sep 2020 11:11:27 +0100

If you have a problem launching Jalview that results in an error message on the splash screen reading:

“We were unable to download the necessary files after five attempts. You can try running the application again, but if it fails you may need to uninstall and reinstall.”

Like this screenshot:

Then you should close the splash screen window and try and launch the Jalview application again.

If this does not work, you should install the latest Jalview release (found at https://www.jalview.org/getdown/release/). The latest installer can be installed on top of the old version.

Can Jalview run with Java 9+

Mon, 20 Nov 2017 16:43:29 +0000

Jalview is compatible with Java 11 and later, but only if you have downloaded and installed a Java 11 compatible Jalview distribution. For now, our recommended distributions run Jalview under Java 8.

If you have installed Jalview via InstallAnywhere and you cannot access JABAWS services (a dialog box appears after you start Jalview about this), then you can patch the Jalview installation.

I downloaded the Jalview Installer for OSX but the install application won't run

Wed, 31 Oct 2012 09:05:38 +0000

The OSX InstallAnywhere version of Jalview is downloaded as a ZIP archive (install.zip) which is normally unpacked automatically to create an application called ‘install’ that you can run. If nothing happens when you double click the application, then there are a few things that could go wrong.

Installer doesn’t launch because it was unpacked with a third-party archive tool

If you have chosen an alternative archive program for OSX to use to unpack ZIP files, then it probably didn’t set the executable permissions for the application after it unpacked it. Theeasiest solution is to right or option click the install.zip that you downloaded, and choose ‘Open with -> Archive Utility (10.X)’ (where X is the numeric version of OSX that you are running); this will create a new ‘install’ application (probably called ‘install 2’) that you can now launch.

I'm having problems using InstallAnywhere on Mac OSX 10.3.9

Mon, 02 Jul 2012 13:02:44 +0100

There is a Mac OS X bug that affects InstallAnywhere LaunchAnywheres on OS X 10.3.9 systems with the QuickTime 7.0.4 upgrade.

This appears to only affect systems running 10.3.9, and not 10.4. The current workaround is to revert to QuickTime 7.0.1, through a reinstaller available from Apple on the Support/Downloads page.

http://www.apple.com/support/downloads/quicktime701reinstallerforquicktime704.html

Is there a quick reference for Jalview?

Mon, 02 Jul 2012 12:51:09 +0100

Yes, a quick reference PDF for an early release of Jalview 2 is here, but we haven’t updated it for a while.

Jalview 2.11.5.2 Installers

Tue, 14 Jul 2026 00:00:00 +0000

Jalview 2.11.5.1 Installers

Wed, 10 Dec 2025 00:00:00 +0000

Type

Installer (Jalview 2.11.5.1 - 10 December 2025)

Installation notes

Your platform has been detected as unknown. Click on the a Download button, or expand the table to view all installers

Your platform has been detected as unknown. Jalview currently only has desktop installers.

Jalview 2.11.5.0 Installers

Tue, 26 Aug 2025 00:00:00 +0000

Type

Installer (Jalview 2.11.5.0 - 26 August 2025)

Installation notes

Your platform has been detected as unknown. Click on the a Download button, or expand the table to view all installers

Your platform has been detected as unknown. Jalview currently only has desktop installers.

Jalview 2.11.4.0 Installers

Wed, 18 Sep 2024 00:00:00 +0000

Type

Installer (Jalview 2.11.4.0 - 18 September 2024)

Installation notes

Your platform has been detected as unknown. Click on the a Download button, or expand the table to view all installers

Your platform has been detected as unknown. Jalview currently only has desktop installers.

Introduction to Jalview

Thu, 05 Sep 2024 00:00:00 +0000

The ‘Introduction to Jalview’ course is aimed at PhD students and post-doctoral researchers with little to no experience of the creation and analysis of multiple sequence alignments (MSAs) and their exploration in the context of predicted and observed 3D structures. It’s also a great opportunity for more experienced users to refresh their knowledge and learn about the latest features in Jalview 2.11.4. As an introductory level course, it is designed to be aligned with the needs of those completely unfamiliar with Jalview’s core capabilities. Advanced level courses will be advertised in the future - please keep an eye out on Jalview’s website.

Administrator Install on Linux

Mon, 26 Aug 2024 00:00:00 +0000

Installer wizard GUI launch

To run the Linux installer in Administrator mode the installer must be launched either by root or through using sudo. e.g.

$

sudo bash ~/Downloads/jalview-2_11_5_1-linux-x64-java_8.sh

Administrator Install on macOS

Mon, 26 Aug 2024 00:00:00 +0000

DMG installation

An Administrator user can now install Jalview in a system location (e.g. /Applications) in a multi-user environment by opening the macOS DMG and dragging it to the Applications folder icon. This will install with all the default options for user-space updates, and users who run Jalview from here will get updates in their own userspace (in ~/Library/Application Support/Jalview-Desktop/Jalview/HASH/app, where HASH is an 8 character SHA256 hash of the app directory found in the App bundle (e.g. /Applications/Jalview.app/Contents/Resources/app hashes to bb307bce).

Administrator Install on Unix

Mon, 26 Aug 2024 00:00:00 +0000

Installer wizard GUI launch

To run the Unix installer in Administrator mode the installer must be launched either by root or through using sudo. e.g.

$

sudo bash ~/Downloads/jalview-2_11_5_1-unix-java_8.sh

Administrator Install on Windows

Mon, 26 Aug 2024 00:00:00 +0000

Installer wizard GUI launch

When the Windows installer is run by an Administrator user in GUI mode (e.g. by the usual double click) the installer will prompt for Administrator rights in the usual way. If Administrator rights are granted then the installer will go into Administrator mode.

This will be noted in bold at the top of the installer. If you don’t see this then the installer is not in Administrator mode.

Jalview 2.11.3.3 Installers

Wed, 22 May 2024 00:00:00 +0000

Type

Installer (Jalview 2.11.3.3 - 21 May 2024)

Installation notes

Your platform has been detected as unknown. Click on the a Download button, or expand the table to view all installers

Your platform has been detected as unknown. Jalview currently only has desktop installers.

Jalview 2.11.3.2 Installers

Fri, 01 Dec 2023 00:00:00 +0000

Jalview 2.11.3.1 Installers

Wed, 22 Nov 2023 00:00:00 +0000

Jalview 2.11.3.0 Installers

Wed, 15 Nov 2023 00:00:00 +0000

Type

Installer (Jalview 2.11.3.0 - 15 November 2023)

Installation notes

Your platform has been detected as unknown. Click on the a Download button, or expand the table to view all installers

Your platform has been detected as unknown. Jalview currently only has desktop installers.

Introduction to Jalview

Wed, 09 Aug 2023 00:00:00 +0000

The introduction to Jalview course is aimed at PhD students and post-doctoral researchers who have little or no experience with the creation and analysis of multiple sequence alignments and their exploration in the context of predicted and observed 3D structures. It’s also a great opportunity for more experienced users to refresh their knowledge and learn about the latest features in Jalview 2.11.3.

This course takes place over two afternoons on 4th and 5th October 2023 at the University of Dundee School of Life Sciences’ Small Lecture Theatre, held in partnership with the School’s PhD program. The course is free of charge, but since spaces are limited, priority will be given to new PhD students affiliated with the University of Dundee and other Scottish universities.

Jalview 2.11.2.7 Installers

Fri, 30 Jun 2023 00:00:00 +0000

Jalview 2.11.2.6 Installers

Mon, 23 Jan 2023 00:00:00 +0000

Import VCF Files & Filter Variant Features

Thu, 12 Jan 2023 00:00:00 +0000

Genome to Function 3. Import VCF Files & Filter Variant Features

(A) Preparation - Download the following files by clicking on these links.

(B) Open a locus view for a gene and its linked CDS/Protein view

Import ‘ENSG00000113924’ into Jalview from the Ensembl database via File ⇒ Fetch Sequences ⇒ ENSEMBL. Transcripts are shown aligned to the reference genome locus.
Open the Protein-CDS split-screen view by selecting Calculate ⇒ Get Cross-References ⇒ UNIPROT.

View Ensembl Features on Protein-CDS Alignments

Thu, 12 Jan 2023 00:00:00 +0000

Genome to Function 2. View Ensembl Features on Protein-CDS Alignments

(A) Import gene from Ensembl database

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.
Transcripts are shown aligned to the reference genome locus. Select Calculate ⇒ Get Cross-References ⇒ UNIPROT to open the Protein-CDS split-screen view.

View Protein Sequence & its Coding DNA

Thu, 12 Jan 2023 00:00:00 +0000

Genome to Function 1. View Protein Sequence & its Coding DNA

Load sequence alignment, select File ⇒ Input Alignment ⇒ From URL in the desktop menu and enter https://www.jalview.org/tutorial/unaligned.fa and click OK.
Load annotation, select Web Service ⇒ Fetch DB References ⇒ From EMBL to UNIPROT ⇒ UNIPROT.
To toggle the sequence features on and off, select View ⇒ Show Sequence Features in the alignment menu.
To view the feature types, select View ⇒ Feature Settings… and this opens the Sequence Feature Settings dialog box . Click OK to close it.

Aligning Structures Ferredoxin

Fri, 07 Oct 2022 00:00:00 +0000

Aligning Structures using the Ferredoxin Sequence Alignment

Continue with the Jalview project created in previous exercise.
Select the FER1_MAIZE sequence (near bottom of the alignment). Right-click the ID label to open the context menu, select $\Rightarrow$ 3D Structure Data.
This opens the Structure Chooser dialog, pick 1gaq or 3b2f from the list. Make sure the Superpose option is checked before clicking the Add button. This superimpose the structure associated with FER1_MAIZE with the one associated with FER1_SPIOL. Note: The Jmol view should update to show both structures, and one will be moved on to the other. If this doesn’t happen, use the Align function in the Jmol submenu.

Colouring Domain Interfaces

Fri, 07 Oct 2022 00:00:00 +0000

Colouring a Protein Complex to Explore Domain-Domain Interfaces

Download the PDB file at https://www.jalview.org/tutorial/DNMT1_MOUSE.pdb to your desktop. This is the biological unit for PDB ID 3pt6, as identified by the PDBe’s PISA server.
Retrieve the following PFAM alignments PF02008, PF01426 and PF00145 separately from the PFAM (full) source into their own alignment window.
Drag the URL or file of the structure you downloaded in step 1 onto one of the alignments to associate it with the mouse sequence in that Pfam domain family.

Editing

Fri, 07 Oct 2022 00:00:00 +0000

Editing Alignments

You are going to manually reconstruct part of the example Jalview alignment available at https://www.jalview.org/examples/exampleFile.jvp. Mac Users: Please use the Apple or [CMD] key in place of [CTRL] for key combinations such as [CTRL]-A.

Remember to use [CTRL]-Z to undo an edit, or the File $\Rightarrow$ Reload function to revert the alignment back to the original version if you want to start again.

Load the URL https://www.jalview.org/tutorial/unaligned.fa which contains part of the ferredoxin alignment from PF03460.

Group Conservation

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Group Conservation Analysis

In the View menu in the alignment window, select New View to create a new view (View 1).
Ensure the annotation panel is displayed (Annotations $\Rightarrow$ Show Annotations is toggled on).
Enable the display of consensus annotation rows for each group by selecting the option in the Annotation $\Rightarrow$ Autocalculated Annotation $\Rightarrow$ Group Consensus.
Displaying the sequence logos makes it easier to see the different residue populations within each group. Activate the logo by right clicking the name of the Consensus annotation to open the context menu and select the Show Logo option.

Keyboard

Fri, 07 Oct 2022 00:00:00 +0000

Keyboard Edits

This continues on from the previous exercise, and recreates the final part of the example ferredoxin alignment from the unaligned sequences using Jalview’s keyboard editing mode.

Window users: Please only use [SHIFT]-[SPACE] in this exercise.

Mac users: [CTRL]-[SPACE] can also be used instead of [SHIFT]-[SPACE].

Load the sequence alignment at https://www.jalview.org/tutorial/unaligned.fa, or con- tinue using the edited alignment. If you continue from the previous exercise, first right click on the sequence ID panel and select Reveal All. Enter cursor mode by pressing [F2] (or [Fn]-[F2] (Mac)).

Redundant Sequences

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Remove Redundant Sequences

Using the alignment generated in the previous exercise. In the alignment window, you may need to deselect groups using [ESC] key.
In the Edit menu select Remove Redundancy to open the Redundancy threshold selection dialog box. Adjust the redundancy threshold value, start at 50 and increase the value to 62. Sequences selected will change colour in the Sequence ID panel. Select Remove to remove the sequences that are more than 62% similar under this alignment.

Tree-Based Conservation

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Tree Based Conservation Analysis

Load the PF03460 PFAM seed alignment using the sequence fetcher. Select Colour $\Rightarrow$ Taylor $\Rightarrow$ By Conservation, set Conservation shading threshold at around 20.
Build a Neighbour joining tree by selecting Calculate $\Rightarrow$ Tree or PCA... in the align- ment window. In the dialogue box, select Neighbour Joining and in the drop-down list select BLOSUM62, then click the Calculate button.
Use the cursor to select a point on the tree to partition the alignment into groups.

User Defined

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