3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>What's new ?</title>
27 <strong>What's new ?</strong>
30 Jalview 2.8.2 is the first release produced by our new core
31 development team.<br /> It incorporates many minor improvements and
32 bug-fixes, and new features for working with 3D structure data,
33 shading alignments by secondary structure and generation of alignment
34 figures as Scalable Vector Graphics. <br />The majority of
35 improvements in this version of Jalview concern the desktop
36 application. As ever, the highlights are detailed below,
37 and the full list is given in the <a
38 href="releases.html#Jalview.2.8.2">Jalview 2.8.2 Release Notes</a>.
41 <strong>Annotation visualisation</strong> <br /> The alignment window
42 includes a new <em>Annotations</em> menu which provides controls for
43 the layout and display of sequence, group and alignment associated
44 annotation rows. It also now includes the <em>Autocalculated
45 Annotation</em> submenu (formerly located in the View menu), which
46 includes settings for the calculation and display of sequence
47 consensus, logos, and amino acid conservation for the alignment and
51 <strong>Sequence associated annotation</strong><br /> New controls
52 have also been added to the Sequence ID popup menu for the propagation
53 and display of sequence associated annotation such as secondary
54 structure assignments and disorder predictions. Annotation associated
55 with one or a group of sequence already shown on the alignment may be
56 shown or hidden, and any available annotation from 3D structure or
57 calculations performed in other Jalview windows can be copied to the
59 <em>via</em> the <strong>Add Reference Annotation</strong> option.<br />
60 The <strong>Colour by annotation</strong> function has also been
61 improved, allowing secondary structure annotation to be used to shade
62 sequences and alignment columns. Protein sequences can be coloured
63 according to the presence of a helix or sheet at each position, and
64 RNA sequences can be shaded according to each structure's stem/helix
65 pattern - which enables different RNA folding topologies to be quickly
69 <strong>3D Structural data analysis and display</strong><br />
70 Jalview now employs Jmol's PDB data API to retrieve secondary
71 structure assignments made by the DSSP algorithm. It can also employ
72 web services to obtain secondary structure assignments from RNA
73 structures. These assignments are shown as sequence associated
74 annotation for sequences which have cross-references to the PDB, or
75 have had PDB files associated with them via the <em>Structures</em>
76 submenu of the sequence ID popup menu. The extraction and display of
77 secondary structure and B-factor column annotation is controlled <em>via</em>
78 a new <strong>Structure</strong> tab in the Jalview Desktop's
79 Preferences dialog box.
82 <Strong>Interoperation with UCSF Chimera</Strong><br /> The desktop
83 application can now be configured to employ UCSF Chimera for the
84 display of 3D structure data. UCSF Chimera is a python-based
85 high-performance molecular graphics and animation system developed by
86 the Resource for Biocomputing, Visualisation, and Informatics at the
87 University of California.<br />Jalview employs the 'StructureViz'
88 communication mechanism developed for Cytoscape by Morris et al.
89 (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
90 allows Jalview to send commands to Chimera, enabling structures to be
91 superimposed and shaded according to associated multiple aligmment
92 views. <br />Support for Chimera in Jalview 2.8.2 is experimental, and we
93 would appreciate feedback ! Please send your comments to
94 jalview-discuss@jalview.org, and keep up to date with this feature's
95 development via http://issues.jalview.org/browse/JAL-1333.
98 <strong>Export of alignment figures as Scalable Vector
99 Graphics</strong> <br />Scalable Vector Graphics (SVG) files are now widely
100 supported by web browsers and graphics design programs, and allow
101 high-quality graphics for interactive exploration and publication.
102 Jalview now supports the generation of SVGs interactively (via the
103 Export) menu, and from the command line for server-side figure