Nucleotide info
These preferences apply only to nucleotide sequences.
The data points for graph representations can be exported (see Export graph data points to a file).
- Translation. Displays a translation into protein just below the nucleotide sequence. Depending on the zoom level, the amino acids are displayed with three letters or one letter. In cases where variants are present in the reads, synonymous variants are shown in orange in the translated sequence whereas non-synonymous are shown in red.
- Frame. Determines where to start the
translation.
- ORF/CDS. If the sequence is annotated, the translation will follow the CDS or ORF annotations. If annotations overlap, only one translation will be shown. If only one annotation is visible, the Workbench will attempt to use this annotation to mark the start and stop for the translation. In cases where this is not possible, the first annotation will be used (i.e. the one closest to the 5' end of the sequence).
- Selection. This option will only take effect when you make a selection on the sequence. The translation will start from the first nucleotide selected. Making a new selection will automatically display the corresponding translation. More about selecting.
- +1 to -1. Select one of the six reading frames.
- All forward/All reverse. Shows either all forward or all reverse reading frames.
- All. Select all reading frames at once. The translations will be displayed on top of each other.
- Table. The translation table to use in the translation. For more about translation tables, see Translate from DNA or RNA into proteins.
- Only AUG start codons. For most genetic codes, a number of codons can be start codons (TTG, CTG, or ATG). These will be colored green, unless selecting the "Only AUG start codons" option, which will result in only the AUG codons colored in green.
- Single letter codes. Choose to represent the amino acids with a single letter instead of three letters.
- Frame. Determines where to start the
translation.
- Quality scores. For sequencing data containing quality scores, the quality score information can be displayed along the sequence.
- Show as probabilities. Converts quality scores to error probabilities on a 0-1 scale, i.e. not log-transformed.
- Foreground color. Colors the letter using a gradient, where the left side color is used for low quality and the right side color is used for high quality. The sliders just above the gradient color box can be dragged to highlight relevant levels. The colors can be changed by clicking the box. This will show a list of gradients to choose from.
- Background color. Sets a background color of the residues using a gradient in the same way as described above.
- Graph. The quality scores are displayed as a graph.
- Height. Specifies the height of the graph.
- Type. The graph can be displayed as Line plot, Bar plot or as a Color bar.
- Color box. For Line and Bar plots, the color of the plot can be set by clicking the color box. For Colors, the color box is replaced by a gradient color box as described under Foreground color.
- Trace data. See Import and view trace data.
- G/C content. Calculates the G/C content of a part of the sequence and shows it as a gradient of colors or as a graph below the sequence.
- Window length. Determines the length of the part of the sequence to calculate. A window length of 9 will calculate the G/C content for the nucleotide in question plus the 4 nucleotides to the left and the 4 nucleotides to the right. A narrow window will focus on small fluctuations in the G/C content level, whereas a wider window will show fluctuations between larger parts of the sequence.
- Foreground color. Colors the letter using a gradient, where the left side color is used for low levels of G/C content and the right side color is used for high levels of G/C content. The sliders just above the gradient color box can be dragged to highlight relevant levels of G/C content. The colors can be changed by clicking the box. This will show a list of gradients to choose from.
- Background color. Sets a background color of the residues using a gradient in the same way as described above.
- Graph. The G/C content levels are displayed as a graph.
- Height. Specifies the height of the graph.
- Type. The graph can be displayed as Line plot, Bar plot or as a Color bar.
- Color box. For Line and Bar plots, the color of the plot can be set by clicking the color box. For Colors, the color box is replaced by a gradient color box as described under Foreground color.
- Secondary structure. Allows you to choose how to display a symbolic representation of the secondary structure along the sequence.
See Import and view trace data for a detailed description of the settings.