Figure 2

The SearchSmallRNA platform. The main window of the program is shown at the center of the figure. Key functions and menus are labeled as A-F. A - Example of a graphical representation of the reads distribution by size. The total numbers of unique reads of all vsRNAs from size classes of 18–26 nts are shown on the X-axis. B – Example of the distribution graph of positive reads along the reference genome. Reads matching the genome in the sense orientation are shown in gray and those in the antisense orientation are shown in yellow. The X-axis shows the total number of reads. The red bar below shows where the putative genome generated matches the reference genome; C – Nucleotide composition command compares differences between mapped and reference genome. Users can visualize easily gaps and nucleotide divergences that are shown in different colors; D – Example of a graphical analysis of the terminal nucleotide from the positive reads/vsRNAs. E – Result windows showing the details of each read mapped; and F – A combination box that allows the user to choose how many mismatches between the read and the reference genome will be allowed in the analyses.