X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=1743f1c4fb6a7bf3589622812bf26752e8218d32;hb=739e52dd5387687cce4831eaafa24116dcaddcb9;hp=e1b00c4d8cc42b2cac8f7202446613fce070e204;hpb=91d4b1d51f21a72c9e3cfa8532e795272851bca1;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index e1b00c4..1743f1c 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -37,16 +37,16 @@
Ensembl sequence fetcher. Annotated Genes,
transcripts and proteins can be retrieved via Jalview's new Ensembl REST
- client. Support for import of Ensembl data also allows:
+ client. Support for import of Ensembl data allows:
- Sequence variant data. Jalview
- propagates variant annotation imported via Ensembl onto
+ 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.
+ their reference genome, and introns hidden from the view.
Working with structures.
@@ -59,15 +59,19 @@
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
+ 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 based alignment
- visualisation.. 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.
-
+ 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.