(note that for SEQUENCING, you should use the dedicated sequencing functions within DNADynamo, NOT the global multiple alignment options)
DNADynamo can send DNA or PROTEIN sequences to the ClustalW or MUSCLE multiple alignment programs, and display the result.
If your sequences are annotated, and you initiate alignments from open DNADynamo sequence windows (see below), annotations are drawn on the sequences in the multiple alignments.
For example, if you have annotated the position of the active site in an enzyme, and then perform an alignment
to several other related enzymes it is easy to locate the active site in the alignment and how the sequences in this region are aligned.
You can then also annotate sequences from within the alignments, and these annotations are added to the sequences in the DNADynamo windows that were used to
generate the alignments.
Example Annotated Alignment
There are three entry points for selecting sequences for Multiple Alignment
1) You can select from sequences that are present in DNADynamo windows that are currently open
For example, if you have three open windows containing DNA sequence that you want to align, press the 'Alignment' button on the main panel of one of the windows, then choose, for example, 'Global Multiple Sequence Alignment
via ClustalW interface' -> 'Align DNA' or 'Align PROTEIN'. (DNA sequences are translated to protein prior to alignment based on their set translation start and stop points)
2) You can use the file 'Manager', accessed by pressing the 'Manager' button on the main window, to select multiple sequence files within a folder. Send them for
alignment by pressing the 'Alignments' button within the Manager, and selecting the alignment option you want to use.
3) You can open file formats that contain multiple sequences eg FASTA or NEXUS files, in the alignment editor. You can choose to either re-align the sequences,
or just open the sequences retaining any existing gaps
Alignment editing is best achieved from the 'Alignment Editor'. If the alignment is displayed in 'Paged' view, press the 'Editor' button first to access the Editor.
You can use editing buttons to insert or delete gaps. Gaps are inserted or deleted to either side of the current cursor position, with the direction of editing
being indicated by the direction arrows on the button. eg 'Insert >' inserts a gap to the right of the cursor while '< Delete' deletes a gap to the left of the cursor.
It is also possible to drag the currenty selected sequence to the left or right using the mouse, or by using the 'Shift' buttons. You can select the entire sequence using the 'Ctrl-A' select all keyboard shortcut.
In paged view, limited editing is available. You can manually edit the position of residues relative to gaps in the alignment by placing the cursor on the residue to be moved,
and holding down the 'shift' key while pressing the right or left arrow keys.
In the editor, you can manually adjust the order of sequences in the alignment by holding down the shift KEY and draging a sequence up or down. You can also use the 'Alignment Options'
-> 'Order Alignments' menu options to eg sort alphabetically, by size, and into groups, based on the currently selected sequence.
In 'paged' view you may change the relative order of sequences in the alignments by placing the cursor on the sequence to be moved, and holding down the 'shift' key while pressing the 'up' or 'down' arrow keys.
You may export alignments to the system clipboard, and subsequently paste them into other software (eg word processor - drawing software)
though note that the alignments are pasted as text only - the annotations graphics are not included.
Use menu option 'File' -> 'Export as Text'
You may however print to pdf and import the pdf into dedicated illustration software such as Adobe Illustrator. Depending on your operating system, you may need to have a PDF print driver installed.
From 'paged' view, first select the 'print size' check box, then press the 'Print' button. From the 'Editor', select 'Print Alignment' - (DNA only)
You may find it necessary to adjust the size of the annotation text before printing. You can do this using the 'Adjust Annotation Display Settings' control panel that is opened under the 'Annotation Display Settings' menu option.
You can save alignments from the 'Editor' by selecting 'SAVE' from the file menu. If you have an annotated alignment created from open DNADynamo sequence files, saving DOES NOT
currently save the annotation information, as this is stored in the open windows. The ability to save annotation information in the saved alignments may be implimented in the future is there is
interest in this function.
The length of sequences that can be aligned will depend on your computers memory. Long sequences may take some time for clustalw to process. If clustalw hangs
you may need to close DNADynamo and try again with a shorter sequence.