What's new in Jalview 2.10.0b1 ?

Jalview 2.10.0b1 is a patch release for 2.10, the next major release in the Jalview 2 series. Full details are in the Jalview 2.10b1 Release Notes, but the highlights are below.

• Drag and drop reinstated for the Jalview desktop on Windows, Linux and older OSX systems.
• Problems loading local PDB files have been fixed
• Conservation shading can be disabled for PID and consensus based colour scheme

Major highlights of the 2.10.0 Release

• 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:
  • Aligned locus view
    Transcripts retrieved for a gene identifier via the Ensembl or EnsemblGenomes sequence databases are automatically aligned to their reference genome, and introns hidden from the view.
  • Sequence variant data
    Jalview propagates variant annotation on genomic regions onto transcripts and protein products, complete with associated metadata such as clinical significance.
• Ensembl and ENA 'show cross-references' support
  The Calculations menu's 'Show cross-references' now offers Ensembl as well as EMBLCDS and Uniprot when CDS/Protein mapping data is available for download or display. This allows variant annotation to be added directly to an alignment of UniProt sequences.
• Working with structures
  • More accurate structure mappings
    Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) to match structures to UniProt sequences, even for structures containing multiple copies of a sequence.
  • Import structures as mmCIF
    Jalview now downloads data from the EMBL-EBI's PDBe site as mmCIF. This allows very large structures to be imported, such as the HIV virus capsid assembly.
  • Chimera users will need to upgrade to 1.11.1
    If you use Chimera to view structures downloaded by Jalview 2.10, you will need to make sure you are running the latest version of Chimera.
• UniProt Free Text Search
  The new search dialog for UniProt allows you to browse and retrieve sequences with free-text search, or structured queries.
• Reference sequence alignment view
  Jalview 2.9 introduced support for reference sequences. In 2.10, when a reference sequence is defined for the alignment, the alignment column ruler is now numbered according to the reference sequence. The reference sequence for alignment views can also be saved and restored from Jalview projects.