At the lower right corner of the Frames window, there are six additional buttons. Click on the button labeled (red circle in Figure 4.8). ‘ORFs’ Figure . This will highlight all the features currently in your feature table as shown in the screenshot above. Genes in forward reading frames are green, those in reverse reading frames are red, and tRNAs are blue. Next click on the frames window within the box that contains a highlighted gene. Figure . A thin, horizontal green line will appear that extends from the nearest upstream start codon to the next downstream stop codon. Now click on the (ribosomal binding site) button in the bottom right corner of the ‘RBS’ Frames window. Figure . Another window titled ORF will appear, shown in Figure 4.11. “Choose Figure . This window lists all of the possible start codons in the ORF you clicked on in the Frames window, the corresponding upstream nucleotide sequence, the gene length resulting from that start, and a score for the Shine-Dalgarno sequence (higher is better). One line’s text may be red, and this is because that row corresponds to the start site immediately upstream of where you clicked in the Frames window. When evaluating your gene calls and choosing between possible start sites, you may find it helpful to have all three windows open at once, as shown in Figure 4.12 for the Etude genome. Figure .
At the lower right corner of the Frames window, there are six additional buttons. Click on the button labeled ‘ORFs’ (red circle in Figure 4.8). Figure . This will highlight all the features currently in your feature table as shown in the screenshot above. Genes in forward reading frames are green, those in reverse reading frames are red, and tRNAs are blue. Next click on the frames window within the box that contains a highlighted gene. Figure . A thin, horizontal green line will appear that extends from the nearest upstream start codon to the next downstream stop codon. Now click on the ‘RBS’ (ribosomal binding site) button in the bottom right corner of the Frames window. Figure . Another window titled “Choose ORF will appear, shown in Figure 4.11. Figure . This window lists all of the possible start codons in the ORF you clicked on in the Frames window, the corresponding upstream nucleotide sequence, the gene length resulting from that start, and a score for the Shine-Dalgarno sequence (higher is better). One line’s text may be red, and this is because that row corresponds to the start site immediately upstream of where you clicked in the Frames window. When evaluating your gene calls and choosing between possible start sites, you may find it helpful to have all three windows open at once, as shown in Figure 4.12 for the Etude genome. Figure .