Archived Jalview News Items (2011-2021)

• New video added to Jalview's YouTube 'Analysis and Annotation' playlist

  25th October 2017 in training news

  Protein disorder predictors in Jalview video has been added to the Jalview YouTube Channel in the Analysis and Annotation playlist, alongside Multiple Sequence Alignment and Analysis with Jalview, Principal components analysis of protein and nucleotide alignments in Jalview, Calculating and Displaying Trees in Jalview, 3D molecular structure Jmol and UCSF Chimera viewers in Jalview, Secondary structure prediction of proteins in Jalview.

• Jalview 2.10.2b1 Released

  7th September 2017 in development news

  A bugfix release for 2.10.2 is now available. Version 2.10.2b1 has the following new features:

  • Show gaps in overview window by colouring in grey (sequences used to be coloured grey, and gaps were white)
  • Overview tab in Jalview Desktop Preferences
  • Overview updates immediately on increase in size and progress bar shown as higher resolution overview is recalculated

  Several minor (and not so minor) bugs are also resolved, including problems with retrieval of Ensembl crossreferences for Uniprot sequences, and PDB sequence/structure associations.

  Read more →

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

  17th August 2017 in development news

  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    Menu entries for calculating PCA and different types of tree have been replaced by a single Calculations dialog box.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.

    Read more →

• Thanks to all attendees of the CBBU Jalview course at ANU!

  23rd June 2017 in training news

  Many thanks to Marcin Adamski of CBBU(and JCSMR) and Rob Lanfear for hosting a one day Jalview workshop at the ANU’s Sciences Teaching Building. Particants included delegates from John Curtin’s Medical School, the Research School of Biology, CSIRO (Canberra), and University of Canberra, and together represented a range of disciplines including mammalian ecology, parasite genomics, biological statistics and precision medicine.

  

• Video added to the Analysis and Annotation playlist on the Jalview YouTube channel

  19th May 2017 in training news

  A video on Secondary structure prediction of proteins in Jalview has been added to our YouTube channel. JPred predicts the location of secondary structure (α-helix and β-strand) and solvent accessibility from a single sequence of multiple alignment.

• Three training workshops in one week

  2nd March 2017 in training news

  The Jalview team were busy last week. Jim Procter and Suzanne Duce ran the one-day Jalview training workshop at the University of Dundee on Wednesday 22th February and the University of St Andrews on Friday 24th February. Geoff Barton ran a protein sequence analysis and structure prediction workshop on Thursday with help from Stuart MacGowan and Fabio Maderia at the University of Dundee. Thanks to Rebeca Diaz Vazquez for the invitation and help setting up the St Andrews workshop.

  Read more →

• Registration for St Andrews Jalview Workshop on 24th February is open!

  3rd February 2017 in training news

  The next Jalview training event is a one day course on 24th February, hosted by The University of St. Andrews’ School of Medicine, and will take place in the Bute Building’s IT teaching room (A21).

  The day starts at 9.15am, and we’ll be covering essential Jalview skills (creating and analysing alignments, calculating trees, and working with features and annotation). We’ll also explore some of the more advanced features for working with 3D structures, linking coding and non-coding nucleotide alignments, and integrating annotation from Ensembl.

  Read more →

• Jalview 2.10.1 Released!

  29th November 2016 in desktop news

  Jalview 2.10.1 is now available from www.jalview.org. This is a minor release in the 2.10 series, and brings a range of bug fixes and minor new features including batch BioJS HTML page generation, interactive selection from structure highlights, and alignment conservation analysis. Jalview 2.10.1 is also significantly more memory efficient when working with very wide alignments.

  With the release of Jalview 2.10.1, we also welcome Kira Mourão to the Jalview Authors. Kira joined Jalview’s core development team in October 2016, and this is the first release to include her contributions.

  Read more →

• Mapping genomic sequence variants on to protein structure

  17th November 2016 in general news

  The latest video on our Jalview YouTube channel is a walkthrough video by Dr David Martin. David demonstrates Jalview’s new split frame window that links coding DNA sequences in the exons with protein sequences and structure.

  David shows how Jalview can propagate variant annotation on genomic regions onto transcripts and protein products. Thus it is now possible to use Jalview’s multiple window desktop to view genomic sequence variants (from Ensembl), and directly link these to their protein sequences (from Uniprot), and then map these onto their 3D structure (from PDB).

  Read more →

• Jalview Version 2.10.0 Release

  6th October 2016 in development news

  Jalview Version 2.10.0 is released today!

  Launch from our home page.

  What’s new in Jalview 2.10?

  Jalview 2.10 is the next major release in the Jalview 2 series. Full details are in the Jalview 2.10 Release Notes, but the highlights are below.

  • Ensembl sequence fetcher Annotated Genes, transcripts and proteins can be retrieved via Jalview’s new Ensembl REST client. Support for import of Ensembl data allows:

    Read more →