<title>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong>
- </p>
- <p>
- Jalview 2.8.2 is the first release produced by our new core
- development team.<br /> It incorporates many minor improvements and
- bug-fixes, and new features for working with 3D structure data,
- shading alignments by secondary structure and generation of alignment
- figures as Scalable Vector Graphics. <br />The majority of
- improvements in this version of Jalview concern the desktop
- application. As ever, the highlights are detailed below,
- and the full list is given in the <a
- href="releases.html#Jalview.2.8.2">Jalview 2.8.2 Release Notes</a>.
- </p>
- <p>
- <strong>Annotation visualisation</strong> <br /> The alignment window
- includes a new <em>Annotations</em> menu which provides controls for
- the layout and display of sequence, group and alignment associated
- annotation rows. It also now includes the <em>Autocalculated
- Annotation</em> submenu (formerly located in the View menu), which
- includes settings for the calculation and display of sequence
- consensus, logos, and amino acid conservation for the alignment and
- subgroups.
- </p>
- <p>
- <strong>Sequence associated annotation</strong><br /> New controls
- have also been added to the Sequence ID popup menu for the propagation
- and display of sequence associated annotation such as secondary
- structure assignments and disorder predictions. Annotation associated
- with one or a group of sequence already shown on the alignment may be
- shown or hidden, and any available annotation from 3D structure or
- calculations performed in other Jalview windows can be copied to the
- alignment
- <em>via</em> the <strong>Add Reference Annotation</strong> option.<br />
- The <strong>Colour by annotation</strong> function has also been
- improved, allowing secondary structure annotation to be used to shade
- sequences and alignment columns. Protein sequences can be coloured
- according to the presence of a helix or sheet at each position, and
- RNA sequences can be shaded according to each structure's stem/helix
- pattern - which enables different RNA folding topologies to be quickly
- identified.
- </p>
- <p>
- <strong>3D Structural data analysis and display</strong><br />
- Jalview now employs Jmol's PDB data API to retrieve secondary
- structure assignments made by the DSSP algorithm. It can also employ
- web services to obtain secondary structure assignments from RNA
- structures. These assignments are shown as sequence associated
- annotation for sequences which have cross-references to the PDB, or
- have had PDB files associated with them via the <em>Structures</em>
- submenu of the sequence ID popup menu. The extraction and display of
- secondary structure and B-factor column annotation is controlled <em>via</em>
- a new <strong>Structure</strong> tab in the Jalview Desktop's
- Preferences dialog box.
- </p>
- <p>
- <Strong>Interoperation with UCSF Chimera</Strong><br /> The desktop
- application can now be configured to employ UCSF Chimera for the
- display of 3D structure data. UCSF Chimera is a python-based
- high-performance molecular graphics and animation system developed by
- the Resource for Biocomputing, Visualisation, and Informatics at the
- University of California.<br />Jalview employs the 'StructureViz'
- communication mechanism developed for Cytoscape by Morris et al.
- (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
- allows Jalview to send commands to Chimera, enabling structures to be
- superimposed and shaded according to associated multiple aligmment
- views. <br />Support for Chimera in Jalview 2.8.2 is experimental, and we
- would appreciate feedback ! Please send your comments to
- jalview-discuss@jalview.org, and keep up to date with this feature's
- development via http://issues.jalview.org/browse/JAL-1333.
- </p>
- <p>
- <strong>Export of alignment figures as Scalable Vector
- Graphics</strong> <br />Scalable Vector Graphics (SVG) files are now widely
- supported by web browsers and graphics design programs, and allow
- high-quality graphics for interactive exploration and publication.
- Jalview now supports the generation of SVGs interactively (via the
- Export) menu, and from the command line for server-side figure
- generation.
- </p>
+ <p>
+ <strong>What's new in Jalview 2.10.1 ?</strong>
+ </p>
+ <p>
+ Jalview 2.10.1 was released on 29th November 2016. Full details are
+ in the <a href="releases.html#Jalview.2.10.1">Jalview 2.10.1
+ Release Notes</a>, but the highlights are below. This is also the
+ first release to include contributions from Kira Mourão, who
+ joined Jalview's core development team in October 2016.
+ </p>
+ <ul>
+ <li><strong>More memory efficient</strong><br />We've slimmed
+ down the consensus analysis data structures used by Jalview so
+ even wider alignments can be worked with.</li>
+ <li><strong>Select highlighted region</strong><br />Press 'B'
+ or use the new menu option in the alignment window's Select menu
+ to mark columns containing highlighted regions generated from
+ structure selections, mouse-overs, or resulting from a Find
+ operation.</li>
+ <li><strong>New custom link mechanism for opening URLs
+ for database cross references.</strong><br /> If you have customised URL
+ links in your Jalview preferences, then you may already have seen
+ the <a href="#warning"> warning dialog (see below).</a></li>
+ <li><strong>New command line export option for BioJS
+ MSAviewer</strong><br />A number of small bugs with the HTML export
+ functions from the Jalview desktop were also fixed.</li>
+ <li><strong>Small but significant changes to the
+ physicochemical properties and consensus calculations</strong><br />Threonine
+ is no longer considered a non-hydrophobic residue in the protein
+ conservation calculation, and minor bugs addressed in PID and
+ consensus colouring.</li>
+ <li><strong>Correct display of disulphide bond
+ features</strong><br /> In linked structure views, Jalview would
+ highlight all residues between in addition to the two linked
+ cysteines. The 'select columns by feature' function in the feature
+ settings would also select all intermediate columns.
+ </ul>
+ <p>
+ <strong><a name="warning">Warning dialog about updating
+ your configured URL links</a></strong><br /> In the desktop prior to Jalview
+ 2.10.1, the only way to configure custom links for a particular
+ database cross-reference for a sequence was to give it a name that <em>exactly</em>
+ matched the database source, and a regular expression for filtering
+ out any spurious matches generated when the custom linked was tested
+ against the Sequence's ID string. Since the introduction of the
+ $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for
+ database cross-reference accession strings, and if you have custom
+ links configured, Jalview will raise a warning message so let you
+ know that you may need to update your links to use $DB_ACCESSION$.
+ </p>
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git://source.jalview.org / jalview.git / blobdiff