DNADynamo Sequence Display Interface

Each DNADynamo Sequence Window is divided into two interactive display areas.
The divider between the two displays may be dragged with the mouse to adjust the space given to each display. The upper display generally shows sequence, tables/lists of restriction sites, or notes. The lower display generally shows maps or a separate protein translation. Use the 'Function' buttons to change the displays. The displays are usually linked. eg select enzymes from a table in the upper display to show on a map in the lower display. Select enzymes/annotations/oligos shown on a map in the lower display to display on the sequence in the upper display.
Sequence view controls
The panel directly above the sequence contains view controls that enable you to display the 'complement', 'residue number', and 'translation' below the sequence, and 'restriction sites' above the sequence. You can also 'bunch' codons relative to the translation frame
additional controls let to adjust the font size, line spacing and relative spacing of the sequence to the translation and annotations, and the relative annotation spacing. Annotations font size can be set in menu 'Sequence' -> 'Adjust Sequence Display'
there are shortcuts to set 'circular', 'antiparallel' (reverse-complement), and 'print', 'copy' or 'export' the image as an 'EPS' file, and 'clear' the display of annotations and 'reset' the display setting defaults
Additional view controls can be found in menu option 'Sequence' -> 'Adjust Sequence Display' - which includes an options to adjust the size of the controls in the window
to display 'annotations' under the sequence, press the 'Draw Annotations' button. Ctrl-click or Shift-click the button to colour or shade the annotations in their set colour. Set the colour via the features map using an annotations pop up options menu.
to display 'oligonucleotides' above the sequence, click them in the 'features map' and select 'display oligo hits on DNA sequence' from the pop up options menu
FUNCTION BUTTONS
Sequence - return to DNA sequence display if upper display is showing enzymes tables etc
Absent - table of restriction enzymes which do not cut the DNA sequence
Unique - table of restriction enzymes which cut once in the sequence
All - table of restriction enzymes and the number of times they cut the sequence
Notes - displays notes for the sequence
PrimerPair - sends the sequence to Primer3 and displays the results
File Manager - opens the file manager to preview or select multiple files for alignments etc
Alignments - various options to align the sequence in the window to other sequences
ORFs - Open Reading Frame Map of the sequence - click ORF to set in sequence.
Features - interactive graphic map with relative location of oligos/enzymes and annotations.
Map - interactive linear restriction map of the sequence. Pressing Ctrl-Map opens a separate window. Special display when an MCS is defined
Protein - display the protein translation in the lower display area.
Sequencing Data - return to the alignment editor, if alignments are loaded for the sequence.
Other Controls
Enzymes for use in restriction enzyme analysis functions are selected with the enzyme box selection button
Find sequence by typing the sequence to find in the 'text box' to the right of the 'FIND' buttons, then press 'FIND'
You can enter a 'Genbank' accession number and press the 'GO' button to retrieve the sequence from NCBI (internet connection required)