X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=448430d6afa3682fefa553af124b0750b0df2a49;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=b115385f5db59c5a464ba9dc9a6d2f76268686c6;hpb=82bb69383ab22735cbd3440c670ae0b290fe6afd;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index b115385..448430d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,62 +24,69 @@

- What's new ? + What's new in Jalview 2.10.0b1 ?

- Jalview 2.9 has been in development since December 2014. In addition - to a multitude of bug fixes and minor improvements (both small, and - rather big!), it also brings major new capabilities for codon-level - analysis of protein alignments and the retrieval and manipulation of - structural data.

For the full list of changes, see the - Jalview 2.9 Release Notes. + Jalview 2.10.0b1 is a patch release for 2.10, the next major release + in the Jalview 2 series. Full details are in the Jalview 2.10b1 Release + Notes, but the highlights are below.

- Highlights in Jalview 2.9

Visualisation, editing and analysis of - cDNA and Protein alignments
A new Split View window allows linked - protein and nucleotide sequence alignments to be viewed, edited, - and analysed as one.
cDNA alignments can also be - reconstructed from protein alignments calculated by Jalview's web - services, and update in response to edits in the amino acid view.
To - start experimenting with cDNA/Protein analysis, jut drop a file - containing cDNA sequences which code for, and have IDs matching - proteins in an existing alignment, and Jalview will do the rest.
Enhanced Integration of UCSF Chimera
Jalview - 2.9 provides full support for the use of Chimera to view 3D - structures linked to alignment views in the Jalview Desktop. We've - also included support for saving Chimera sessions in Jalview - project files.
Jalview and Chimera communicate using local - web server connections, which may cause firewall alerts on some - systems, but has the advantage of allowing bidirectional - communication. Communication between Jalview and Chimera is now - much more responsive, and selected regions in Chimera are now - shown as highlighted regions in the Jalview desktop.
Interactive querying of the PDBe
Jalview - users can now browse and retrieve 3D structure data from the PDB - via the PDBe - Search API (Gutmanas - et al 2014). Developed in collaboration with the PDBe group at - EMBL-EBI, the interface allows both structured and free-text - queries to be performed, and allows automatic selection of the - most relevant structures for an alignment acording to a variety of - criteria.
Improved support for RNA visualisation
Jalview - 2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views - can also now be stored in Jalview projects. We've also dealt with - a number of lingering bugs in the VARNA/Jalview interface, - including the loss of pseudoknots when RNA secondary structure is - shown VARNA.
Protein Secondary Structure predictions - with JPred4
Jalview includes a number of new features for working - with secondary structure predictions from the JPred4 server. These - include the ability to automatically hide insertions and highlight - mutations in an alignment with respect to a reference sequence. - Jalview 2.9's new scrollable SVG HTML export was also - developed specifically for the JPred4 server.
Drag and drop reinstated for the Jalview desktop on + Windows, Linux and older OSX systems.
Problems loading local PDB files have been fixed
Conservation shading can be disabled for PID and consensus + based colour scheme

Major highlights of the 2.10.0 Release

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.