X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=c002eb8009144bc6e0ed69d53fabd69b7ad6229a;hb=281aa090976818b388374b7aae780a29a8864b96;hp=545d55b9a780c803a92270b8e96bcbd50176585e;hpb=4497a70ab5bf22b6b6a16c723949625fcca4845b;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 545d55b..c002eb8 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,58 +24,116 @@

- What's new ? + 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.

- Highlights in Jalview 2.10 + 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Menu entries for + calculating PCA and different types of tree have been replaced by + a single Calculations + dialog box.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 proteinsÂ 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 -
- 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 - 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.
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.