Figure 2
From: Exploration of plant genomes in the FLAGdb++ environment
Display of groups of genes in FLAGdb++. (a) The results of queries using blast, gene lists, keywords, protein motifs, gene families or functional categories, are gathered into tables of functional information (content is defined by the user). These tables interact with the genome browser window and provide cross-links and tools in order to download the data, retrieve sequences (genes, CDS, proteins, promoters relative to ATG or TSS), and to display gene structures (see 2b). Here, the example concerns the bHLH transcription factor family in Vitis vinifera. The table presents for each gene, its chromosome, its phylogenetic profile through different phyla (color legend is explained in the pop-up window), the detected PFAM motifs, the number of predicted TM domains, the number of cognate EST/cDNAs, the predicted subcellular localization (scores are available in the pop-up text), and the functional annotation inferred from sequence similarities. (b) A button opens a tool dedicated to gene structures and promoters. The user can remove or sort the genes, choosing whether or not to display the introns, align the structure from ATG or TSS (based on the cognate EST/cDNAs), and look for nucleotide patterns (colored triangles) in the promoter regions.