X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=297233de91dd97a110bee36910d925156a9e8441;hb=9ee29162e3f41c2a60c50f1fda2f3d045adb658f;hp=cab871c874fb5d1f064fdee0a2f225120c0d1636;hpb=4fdcc803d2e906c7f21912d8d004b57589a048be;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index cab871c..297233d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,60 +24,120 @@

- What's new in Jalview 2.10 ? + Jalview 2.10.2b1 bugfix release

- 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. + This is patch release for 2.10.2. See the release notes for full + details bugs addressed in this version, which also introduces + additional improvements to the overview panel, and patches for + several minor issues including the ability to correctly recover + cross-references for Uniprot protein sequences from Ensembl. +

+ What's new in Jalview 2.10.2 ? +

+ Version 2.10.2 was released in August 2017, and introduced new user + interface features, improved and more extensible tree and PCA + analysis, more robust 3D structure viewing with UCSF Chimera and an + updated service client for JABAWS. The full list of bug fixes and + new features can be found in the 2.10.2 Release Notes, but + the highlights are below. +

New dialog and faster and more + configurable Tree and PCA calculations
Menu entries for + calculating PCA and different types of tree have been replaced by + a single Calculations + dialog box. The underlying implementation for the PCA and tree + calculations have been made faster and more memory efficient.
Extensible score models
A new + framework has also been created for the score models used to + calculate distances between sequences and shade alignments. This + framework allows import of substitution matrices in NCBI and + AAIndex format.
PCA Bug Fixes. Jalview's + implementation of PCA differed in its treatment of gaps and + non-standard residues. The BLOSUM62 matrix also included a typo + that affected results. See the 2.10.2 release note + about score model bugs for details and how to reinstate legacy + behaviour.
Update to JABAWS 2.2
Jalview's + alignment, protein conservation analysis, and protein disorder and + RNA secondary structure prediction services are now provided by JABAWS 2.2. + Several of the programs provided as JABAWS 2.2 services have been + updated, so their options and parameters have changed.
URL linkouts to other bioinformatics + databases
New preferences for opening web pages for + database cross-references via the UK Elixir's EMBL-EBI's MIRIAM + database and identifiers.org services.
Showing and hiding regions
Hide insertions in the + PopUp menu has changed its behaviour. Prior to 2.10.2, columns + were only shown or hidden according to gaps in the sequence under + the popup menu. Now, only columns that are gapped in all selected + sequences as well as the sequence under the popup menu are hidden, + and column visibility outside the selected region is left as is. + This makes it easy to filter insertions from the alignment view + (just select the region containing insertions to remove) without + affecting the rest of the hidden columns.
Gap count - a.k.a. the Occupancy + Annotation Row
Another way to filter columns according to + the presence of gaps is to enable the Occupancy + Annotation row via Jalview's Preferences. This annotation row + shows a histogram of the number of aligned residues at each + column. The Select + By Annotation dialog now also includes a percentage threshold + mode, to make it easy to filter alignments to show only those + columns with a particular fraction of aligned sequences.
Recent search history for Find, PDBe and + Uniprot
Easily repeat a previous search for Find and the free + text search system (for querying Uniprot and the PDBe).
Improved Overview Window
The alignment overview is now easier + to use when working with alignments of more than 5000 rows and + columns, and features a new pop-up menu that allows hidden regions + to be excluded from the overview. It also works with CDS/Protein + alignments and MSA views in wrapped mode.
3D Structure
Jalview's communication + with UCSF Chimera has been made more robust, particularly when + working with many structures and long sequences. Regions in + structures that correspond to hidden regions in an alignment view + are now left un-coloured, making it easier to highlight specific + features in 3D. See below for experimental + features for exchanging annotation between Chimera and Jalview.

+ Scripting
New groovy examples + demonstrate Jalview 2.10.2 APIs for creation of data-driven + colourschemes, and custom alignment file handlers. The FeatureAnnotationWorker + introduced in Jalview 2.10 has also been refactored to allow + efficient counting across multiple feature types. Please be aware + that feature counter scripts created for earlier versions will not + execute in Jalview 2.10.2. +

+ Experimental Features +

+ This release of Jalview introduces an Experimental Features + option in the Jalview Desktop's Tools menu that allows you + to try out features that are still in development. To access the + experimental features below - first enable the Tools→Enable + Experimental Features option, and then restart Jalview.

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.
Annotation transfer between Chimera and Jalview
Two + new entries in + the Chimera viewer's Chimera menu allow positional annotation to + be exchanged between Chimera and Jalview.