DNA or RNA sequence can be visualized in three different views: Linear Map, Sequence Map, and Circular Map. Users can switch between these three views by clicking the map name.

Linear Map

As shown below, this will display the sequence as a single-line view in the ‘fit to screen’ scale. The nucleotide sequence is hidden unless the scale in the lower left has been set to maximum. This view will display any Annotation Features, and the ORF can be displayed when turned on in the Display Setting. Translation features, enzymes, and primers are hidden until the scale is set to maximum view.

Sequences devoid of Annotation Features will be displayed as a single linear line

Sequence Map

The Sequence Map provides a multi-line view in the ‘maximum 100 bp per line’ scale. The nucleotide sequence, annotation features, translation features, and primers are all displayed. Enzymes are displayed for DNA sequence only. The ORF can be displayed as well if it is turned on in the display setting.

Circular Map

The Circular Map view of a sequence is only available with circular sequences and will default to the ‘fit to screen’ scale. The nucleotide sequence will be hidden until the scale is set to maximum. Annotation features, enzymes, and primers will be displayed for DNA sequences, while annotation features and primers will be displayed for RNA sequence. ORF can be displayed if it is turned on in the display setting. Translation features are hidden unless the scale is set to maximum.

You can define which elements to show, e.g., toggle on/off sequence and/or its reverse complement; annotation features; enzymes (cut sites); primers; and translation elements (ORFs, translations) by checking/unchecking the element(s) in Display Setting (the Gear icon on the top right of the window).