Screenshots of two windows displaying features in FLAGdb++. (a) In the main window of the FLAGdb++ application, the right panel displays a genome map overview while the left panel shows a detailed local view of 10 Kb in length per line. In this example, the topological organization of the Harbringer repeat elements is displayed over the Arabidopsis genome map. The local view presents the following feature tracks: official mRNA and CDS annotation from TAIR (light and dark blue arrows respectively), PFAM motifs (deep brown arrows), alternative CDS annotation from the EuGène predictor (deep purple arrows), CATMA gene specific tags and Affymetrix ATH1 primers for microarray approaches (purple lines and small vertical red boxes respectively), expertized repeat element annotation (light grey arrows), expertized PPR motifs and gene annotation (yellow and orange arrows) and cognate transcript sequences (small pink circles above the genes: darker means a greater number of cDNA/EST). All the features are associated with specific pop-up menus supplying additional information, tools, and/or cross-links with other resources. ( b) 'Zoom in' upon selection of a specific feature opens a new window displaying additional data (according to the user setting selected through the Feature Manager tool). Represented here are all the splice-aligned cognate transcript sequences, i.e. cDNA and Sanger/454 ESTs (pink arrows), and the available mutant line tags, i.e. T-DNA flanking sequences (red flags). The display of transcript sequence alignments allows the user to detect eventual erroneous annotation or alternative splicing events, as illustrated in this example.