- <li><strong>Ensembl sequence fetcher.</strong> Annotated Genes,
- transcripts and proteins can be retrieved via Jalview's new <a
- href="features/ensemblsequencefetcher.html">Ensembl REST
- client</a>. Support for import of Ensembl data also allows:
- <ul>
- <li><strong>Sequence variant data.</strong> Jalview
- propagates variant annotation imported via Ensembl onto
- protein products, complete with associated metadata such as
- clinical significance.</li>
- <li><strong>Aligned locus view.</strong> Transcripts
- retrieved for a gene identifier via the Ensembl or
- EnsemblGenomes sequence databases are automatically aligned to
- their reference genome.</li>
- </ul></li>
- <li><strong>Working with structures.</strong>
- <ul>
- <li><strong>More accurate structure mappings.</strong>
- 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.</li>
- <li><strong>Import structures as mmCIF</strong>. Jalview
- now downloads data from the EMBL-EBI's PDBe site as mmCIF.
- mmCIF files allow Jalview to handle very large structures,
- such as the HIV virus capsid assembly.</li>
- </ul></li>
- <li><strong>UniProt Free Text Search</strong>. The new search
- dialog for UniProt allows you to browse and retrieve sequences
- from UniProt with free-text search and more structured queries</li>
- <li><strong>Reference sequence based alignment
- visualisation.</strong>. 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.</li>
- <li></li>
+ <li>OSX: The 'Save As' dialog for Jalview's Groovy Console
+ remains affected: the workaround is to create a new file outside
+ of Jalview and then select it when saving your groovy script. We
+ hope to address this in the next major release.</li>
+ <li>OSX: Jalview only displays old news feed items</li>
+ <li>OSX: Users may have to manually configure a web browser
+ helper application ('/usr/bin/open' can be used in the Connections
+ Preferences panel to open URLs with your default browser).</li>