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:
  • Sequence variant data. Jalview propagates variant annotation on genomic regions onto transcripts and protein products, complete with associated metadata such as clinical significance.
  • 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.
• 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 from UniProt with free-text search and more 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.
• Ensembl and ENA 'show cross-references' support.The Calculations menu's 'Show cross-references' will now offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein mapping data is available for download or display.