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.