What's new ?
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.
Highlights in Jalview 2.10
- 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.
- 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.