From: Jim Procter
Date: Wed, 5 Oct 2016 19:58:12 +0000 (+0100)
Subject: JAL-2189 tweak ensembl release notes
X-Git-Tag: Release_2_10_0~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4fdcc803d2e906c7f21912d8d004b57589a048be;p=jalview.git
JAL-2189 tweak ensembl release notes
---
diff --git a/help/html/features/ensemblsequencefetcher.html b/help/html/features/ensemblsequencefetcher.html
index c842a42..e547c58 100644
--- a/help/html/features/ensemblsequencefetcher.html
+++ b/help/html/features/ensemblsequencefetcher.html
@@ -29,16 +29,13 @@
retrieve annotated transcripts, peptides and genomic contigs from
ENSEMBL.
-
+
-
- Two types of ENSEMBL source are provided. ENSEMBL queries the main
- ENSEMBL warehouse containing data for higher eukaryotes, and
+
Two types of ENSEMBL source are provided. ENSEMBL queries the
+ main ENSEMBL warehouse containing data for higher eukaryotes, and
EnsemblGenomes, which queries Ensembl Pathogens, and other
- warehouses.
Ensembl support is new in Jalview, and
- we expect to merge these sources in a future release.
-
+ warehouses.
General Use
If you have a set of Ensembl
gene or transcript IDs, then you can retrieve them via the
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index f8de1f0..cab871c 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -32,52 +32,52 @@
2.10 Release Notes, but the highlights are below.
- 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..
+ 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.
- 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.
-