DNA Sequence

DNA sequence is displayed in the main windows upper display area. You may type or paste in DNA sequence directly (including pasting in an entire genbank record) or import DNA sequence from other sources.

Press the mode button in the top left corner of the display to switch between DNA Only and Translated display modes. To return to the DNA sequence display at any point when the main window is displaying other information, press the Sequence button on the main window buttons panel. Pressing the Sequence button also acts to clear highlights and selected oligos.

To search for subsections of DNA, type bases into the 'Find' text area and press the adjacent 'FindDNA' button. All occurrences of the searched for DNA are highlighted in the main DNA sequence. If the display is in translated or protein mode, you may search for protein sequences using the FindProtein button

To align sequencing data against the sequence, select Open and Align Sequencing Files from the Sequencing pull down menu.

To perform a 'global sequence alignment' of the DNA sequences in open windows, press the 'Alignments' button and select 'global multiple sequence alignment (clustalw or MUSCLES)' -> ' Align DNA'

To display an oligo above the DNA sequence, select the oligo with the mouse from the features graphic map or press 'Location' in the Oligo Box Window. To highlight an annotation, similarly select the annotation from the features map or press the Location button in the Annotation Box.

You can increase the size of the main window by dragging with the mouse or 'maximising' to increase the area available for displaying the DNA sequence. You can also adjust the DNA displays font size using the 'Size Spinner' located at the top of the DNA displays vertical scroll bar.