Jalview 2.10.2 - faster PCAs, better overview, and much more

Posted On: 
17-08-2017

This August 2017 release of Jalview introduces new user interface features, improved and more extensible tree and PCA analysis, more robust 3D structure viewing with UCSF Chimera and an updated service client for JABAWS. The full list of bug fixes and new features can be found in the 2.10.2 Release Notes, but the highlights are below.

  • New dialog and faster and more configurable Tree and PCA calculations
    Menu entries for calculating PCA and different types of tree have been replaced by a single Calculations dialog box. The underlying implementation for the PCA and tree calculations have been made faster and more memory efficient.
  • Extensible score models
    A new framework has also been created for the score models used to calculate distances between sequences and shade alignments. This framework allows import of substitution matrices in NCBI and AAIndex format.
    PCA Bug Fixes. Jalview's implementation of PCA differed in its treatment of gaps and non-standard residues. The BLOSUM62 matrix also included a typo that affected results. See the 2.10.2 release note about score model bugs for details and how to reinstate legacy behaviour.
  • Update to JABAWS 2.2
    Jalview's alignment, protein conservation analysis, and protein disorder and RNA secondary structure prediction services are now provided by JABAWS 2.2. Several of the programs provided as JABAWS 2.2 services have been updated, so their options and parameters have changed.
  • URL linkouts to other bioinformatics databases
    New preferences for opening web pages for database cross-references via the UK Elixir's EMBL-EBI's MIRIAM database and identifiers.org services.
  • Showing and hiding regions
    Hide insertions in the PopUp menu has changed its behaviour. Prior to 2.10.2, columns were only shown or hidden according to gaps in the sequence under the popup menu. Now, only columns that are gapped in all selected sequences as well as the sequence under the popup menu are hidden, and column visibility outside the selected region is left as is. This makes it easy to filter insertions from the alignment view (just select the region containing insertions to remove) without affecting the rest of the hidden columns.
  • Gap count - a.k.a. the Occupancy Annotation Row
    Another way to filter columns according to the presence of gaps is to enable the Occupancy Annotation row via Jalview's Preferences. This annotation row shows a histogram of the number of aligned residues at each column. The Select By Annotation dialog now also includes a percentage threshold mode, to make it easy to filter alignments to show only those columns with a particular fraction of aligned sequences.
  • Recent search history for Find, PDBe and Uniprot
    Easily repeat a previous search for Find and the free text search system (for querying Uniprot and the PDBe).
  • Improved Overview Window
    The alignment overview is now easier to use when working with alignments of more than 5000 rows and columns, and features a new pop-up menu that allows hidden regions to be excluded from the overview. It also works with CDS/Protein alignments and MSA views in wrapped mode.
  • 3D Structure
    Jalview's communication with UCSF Chimera has been made more robust, particularly when working with many structures and long sequences. Regions in structures that correspond to hidden regions in an alignment view are now left un-coloured, making it easier to highlight specific features in 3D. See below for experimental features for exchanging annotation between Chimera and Jalview.

Scripting
New groovy examples demonstrate Jalview 2.10.2 APIs for creation of data-driven colourschemes, and custom alignment file handlers. The FeatureAnnotationWorker introduced in Jalview 2.10 has also been refactored to allow efficient counting across multiple feature types. Please be aware that feature counter scripts created for earlier versions will not execute in Jalview 2.10.2.

Experimental Features

This release of Jalview introduces an Experimental Features option in the Jalview Desktop's Tools menu that allows you to try out features that are still in development. To access the experimental features below - first enable the Tools→Enable Experimental Features option, and then restart Jalview.