A Quick Guide to DNADynamo
If you can't find the answers to your questions in this guide, use the 'Ask A Question' option under the DNADynamo 'File' menu or
email support@bluetractorsoftware.co.uk directly and we will try and answer your questions as soon as we can.
main window interface

DNADynamo helps you work with DNA and PROTEIN sequences
Press the MODE button for a 'translated' display
Adjust the sequence display with the sequence view controls, and 'Draw Annotations' function button
Sequence annotations, oligonucleotides, and notes can be added to each sequence.
Restriction enzyme sites can be displayed as integrated maps and tables and on the DNA sequence display.
Sequencing data can be assembled onto a guide/reference sequence for comparison/mutation analysis, or assembled into a new contig
Vector sequences can be set as 'circular' and auto-annotated against a preset database of common sequences (promoters, resistance genes etc), and displayed as circular maps
Global sequence alignments cab be performed with Clustalw or MUSCLES, and results displayed in a paged display or in the alignment editor, where 'hand made' alignments can be made.
You can BLAST sequences using the NCBI blast interface (internet connection required)
There is a virtual subcloning tool to help you place an 'Insert' sequence into a 'Vector' sequence.
The 'File Manager' lets you preview files in folders, and select multiple files to open, align, batch edit, or export.
Translation Start And Stop Points

Position the cursor, click the right mouse button and select 'Set Translation Start/Stop' or mouse click an ORF in the ORF display.
Sequence Display Modes for DNA and Protein
Pressing the Mode button switches between 'DNA Only' and 'Translated' display Mode

You can edit the protein sequence and select a codon for the corresponding DNA sequence
You may also display protein in the lower display area by pressing the 'Protein' button. DNA and protein sequence displays are linked. eg selecting an amino acid in the protein will highlight the corresponding DNA sequence.
Tables of Restriction Enzyme Sites and Linear Maps
A table is show together with a linked map of unique restriction sites ('All' button and 'Map' button) . Selecting enzymes with multiple cut sites from the table adds them to the graphic map below. Selecting enzymes in the graphic map highlights the restiction enzyme site in the DNA sequence display.

Oligo Editor
An oligo editor helps you design and store oligo sequences - or use the 'PrimerPair'
primer3 interface for primer pairs.
Oligos stored in DNADynamos 'Master Oligo Box' appear on features maps

Circular Maps
You can draw circular annotated maps for sequences that have been set as circular. Select the 'circular' check box in the view controls, or use the Vectors menu 'set as circular' option.

Using Enzyme Boxes
You may use subsets of the available restriction enzymes (boxes) for analysis. Several preset boxes are available such as commonly used enzymes with recognition sites of 6 or more base pairs (common6+). You may also create your own boxes with the enzyme box editor shown below. Enzyme boxes are selected using the Enzyme Box Selection Button' on the main window. You can use menu option 'Restriction Enzymes' -> 'Set Default Enzyme Box' to set the box selected when a new window is opened. Tables of restriction sites, graphic restriction maps, silent mutagenesis results and other displays are automatically updated to reflect the change in enzyme box selection

Features Map
the features map displays the relative location of oligos or enzymes and annotations in the DNA sequence. You can click annotations to bring up a menu of options.
Sequencing Data

You can use DNADynamo to open and align sequencing data files (.abi/.scf trace files or sequences without an associated trace (eg .txt or .fasta etc). You either align the sequences against the sequence in the main window (reference/guide mode) - for comparison to an expected result - or assemble the sequences into a new 'contig'. In the alignments editor, sequence alignments are shown in the upper display area and linked to chromatogram data in the bottom display area. Bases and their alignment positions may be edited using the Alignment Editing buttons at the top of the display.
Virtual Subcloning

The virtual subcloning tool helps you place an 'insert' DNA sequence into a 'Vector' DNA sequence. Select 'Subclone this insert sequence into a vector' from the Vectors pull down menu and the required vector from the list of available vectors on the left. Restriction sites to be ligated are dragged together using the mouse and the 'Create Clone' button opens a new window with the required sequence.