The Genome Browser. (A) A graphical display of 10 kb of the D. purpureum genome. (a) Tabs at the top, Select Tracks, Custom Tracks and Preferences, allow choosing specific genome features, add new ones and customize display preferences. (b) The search box allows to search for any gene name or ID using an auto-complete function, or to enter distinct coordinates. (c) The download menu contains options to display the DNA sequence or as a decorated Fasta file, the position of restriction sites or track data in GFF format. (d) The Data Source drop-down lets the visitor easily switch between genomes. (e) Overview section: this area shows a compressed view of the contig or chromosome. Moving the red box from side to side allows changing the Region Details area without reloading the page. (f) The Region Details area displays the individual chromosomal features in selectable tracks. Tracks shown from top to bottom are as follows: D. purpureum Genes, Gene Models, D. discoideum protein alignments and RNAseq (all time points). (g) A small ruler may be clicked and expanded to assess the exact alignment of sequences. (B) This is an expansion of the Region Details section, showing selected RNAseq data available for the sequence DPU0052717. The top track displays the gene model, all tracks below display RNAseq levels at different developmental time points: 0, 4, 8, 12, 16, 20, 24 and at 48 h after slug migration, pre-stalk cells only. The RNAseq data shows that this gene (the D. purpureum ortholog of the D. discoideum KsrA kinase) is up-regulated at 12 and 16 h, the stage when stalk formation begins. Pre-stalk expression is also confirmed in the 48-h prestalk track at the bottom. The blue color indicates expression above threshold, red indicates low expression below threshold. Also, keep in mind that the scale of the y-axis must be considered when assessing expression levels—GBrowse autoscales each track. (C) When the ‘RNAseq all time points’ are selected and zoomed in to <100 bp, all individual reads of the RNAseq data can be viewed. In this D. purpureum example, 100 bp at an intron/exon boundary are shown, and the RNAseq data indicate that the exon start from the automatic gene prediction (black arrow head) should be moved a few nucleotides upstream to the agT splice acceptor as indicated by the top RNAseq tracks (white arrow head).