It should be released this september or october. It will contains many improvements:
- new icons from the Tango Desktop Project
- a new documentation entirely focused on the construction of 3D models derived from solved 3D structures (as we did for Saccharomyces cerevisiae and Trypanosoma brucei )
- construction of the alignment has been simplified and improved. It is not anymore necessary to add gaps to move residues. Just click on residues, move them and the gaps will be added automatically
- the structural alignment is now made with two bracket notations: the bracket notation derived from the reference structure and a consensus one. The consensus bracket notation is editable and is independent of the reference sequence chosen.
- select a range of contiguous residues in your alignment and Assemble2 will automatically extract a subalignment. This subalignment will be submitted to a new Web service based on the algorithm mlocarna. At the end, you will get a high-quality multiple alignment linked to a consensus structure. This feature was extremely useful for us to have a first draft of 2D for the additional domains of Trypanosoma brucei.
- attach and display numeric values to 2D: this will allow you to visualize your experimental data directly on a 2D (SHAPE, chemical probing, accessibility,..)
- load your data from file or directly from databases using an entry ID. For now, the databases supported are Rfam, RNA STRAND and the Protein Databank
- to speed up Assemble2, you will have the choice to install only the data locally (partial installation) or the data and the Web services (full installation)
- imagine a tool displaying a genomic sequence, its annotations (genes, CDS, introns,..) and the 2D structure of ncRNA annotations in a single window. In summary: Assemble2 = Rfam + NCBI.