The new JV2 software architecture and alignment-rendering model provides the foundation for two JV2 program flavours: JalviewLite (JVL) and Jalview Desktop (JVD). JVL is a web optimized, Java 1.1 compliant applet that replaces Jalview V1.0 where it is used on a web page. In contrast, JVD is a fully-fledged desktop application that can be installed easily on the user's machine and launched in batch or interactive mode from the command line, or started via Java WebStart (Java 1.4 or later). The capabilities of the JVD that are summarized in and described below include the ability to generate high-quality alignment figures for publication, and to exploit web services for data retrieval and analysis. JVL and JVD both utilize Jmol, an open source molecular graphics viewer, to present linked views of PDB files associated with an aligned sequence.
Fig. 1. Capabilities of the Jalview 2 desktop application. Ovals depict major capabilities: visualization, interactive editing, analysis and WYSIWYG figure generation. Arrows connect bioinformatics data handled by JV2 with flat-file or web-service data sources. (more ...)
The core JV2 functionality present in JVL and JVD provides significantly enhanced editing and viewing capabilities when compared to JV1. Interactive editing, colouring and annotation can be performed via the mouse or in a keyboard-editing mode. Alignment edits can be undone, and any number of independent views may be created in tabs or as separate windows opened on the same alignment. Navigation in a view is facilitated by an overview window, and each view also has its own layout and display settings. Specific sequences or columns can be hidden from a view, and arbitrary regions may be selected for analysis either by the built-in algorithms or remote web services, cut or copied to another alignment, or defined as named groups and coloured with one of 11 built-in or user-defined alignment colour schemes, or shaded by conservation or quantitative alignment annotation. Annotation rows may be interactively created and displayed below the columns of the alignment. They may contain labels, secondary structure symbols, coloured histograms or line graphs. Sequence features may also be overlaid onto an alignment. Non-positional information, such as sequence database accession numbers and literature references, are viewed as a tooltip displayed when the mouse hovers over a sequence's ID. Positional features such as metal ion binding sites are rendered as transparent or opaque shading over the visible regions of the alignment. Features may also be edited interactively or created from the results of a regular expression search over the alignment. New JV2 file parsers have been developed to generate annotated alignments from Stockholm alignment files, to import features from GFF, and to read and write Newick formatted phylogenetic trees. Three new formats have also been developed. Sequence regions and groups, colouring and alignment annotation are recorded in Jalview annotation files, whereas Jalview feature files are used to exchange sequence feature annotation. The JVD also supports an additional XML document format, the Jalview Project Archive, which enables all alignments, trees, structures, views and DNA/protein/structure mappings to be recorded and returned to at a later date.
2.1 Embedding JV2 in web applications
), and the structural genomics target optimization pipeline, TarO (Overton et al.
). Interaction with web application developers has been an important influence on development. For example, the sequence feature settings interface arose to support the needs of MACSIMS (Thompson et al.
2.2 Web services access from the Jalview desktop
provides an overview of the capabilities of the JVD. Its primary role is to support alignment creation, editing and in-depth analysis, and enables the visual integration of local and distributed sources of sequence annotation and structural data. Command-line parameters passed via Java Webstart provides a route for the JVD to be launched from the JVL or directly by a bioinformatics web application, but it can also access public sequence, structure and alignment databases with WSDbFetch (Pillai et al.
) to retrieve or transfer database accessions and annotation from their records. Menus on the JVD interface enable the researcher to gather sequence and annotation data from external databases, and utilize Jalview's own dedicated SOAP web services for sequence alignment with ClustalW (Thompson et al.
), Muscle (Edgar, 2004
) and MAFFT (Katoh et al.
) and secondary structure prediction with Jpred3 (Cole et al.
JVD also interacts with Distributed Annotation System (DAS) servers conforming to the DAS 1.53 specification (Dowell et al.
; Prlic et al.
). Sequence and annotation servers can be manually added or discovered from the public DAS server registry. Sequences can be retrieved from or matched against any registered sequence source, and features retrieved from annotation sources mapped onto the alignment sequence's local coordinate frame.