CINEMA (Colour INteractive Editor for Multiple Alignments) is a tool for the visualisation and construction of multiple sequence alignments. It provides a highly intuitive and flexible interface that is consistent with a key UTOPIA design philosophy that underlying technology should not prejudice user experience; the basic means of interaction is the familiar `point and click/drag and drop' metaphor of most office and design applications.

Flexibility of visualisation is a principal attribute of CINEMA: alignments can be shown at different scales within a particular view, from a close-up suitable for detailed editing tasks through to a pixel-per-residue overview. Multiple views of an alignment can be open simultaneously allowing, for example, many different regions of an alignment to be shown at once, or for the same region to be compared at different levels of detail, using separate colour schemes if desired. Basic alignment editing is supported through an intuitive mouse-controlled interface: sequences are aligned simply by dragging them left or right, with gaps automatically inserted or removed as appropriate. This allows the user to concern themselves only with concepts such as `align this bit of the sequence with that bit of that sequence', or `slide this sequence back and forth', rather than `insert 139 gaps here'.

The unique advantage afforded by the underlying model and API is that CINEMA can visualise more than just the sequence-level information traditionally presented by alignment editor applications. If a protein is retrieved from the PDB database, for example, then CINEMA has access to any secondary structure information present; this secondary structure is held as an annotation in the model and can be shown in an appropriate manner alongside the sequence of residues. In fact, CINEMA is able to visualise any arbitrary annotation data present in the data model; the precise nature of that visualisation depends only on how the annotation is structured. For example, annotations representing a set of contiguous extents on the residue sequence, such as conserved sequence motifs, could be drawn as coloured bars below the appropriate section of sequence. Similarly, annotations that consist of continuous values associated with individual residues could be drawn as a graph or spectrum of colours.

You can download the latest version of CINEMA here. There is a comprehensive user guide for CINEMA.