You can open multiple sequences from various sources:
- Several single-sequence files
- One multiple-sequence file
- Several multiple-sequence files, or a combination of single-and multiple-sequence files.
When you open multiple sequences from any of these sources, you may want to open them in individual sequence windows, or in a single MSA editor window.
The default behavior of MacVector is to use the following guidelines when opening one or more sequence files:
MacVector, Staden, RSF, ASCII 1-letter:
-Individual sequence windows
GenBank, EMBL/SWISSPROT or NBRF files, containing single or multiple sequences
- Individual sequence windows
NEXUS, MSF, PHYLIP or FastA (MacVector multiple sequence) files, containing single or multiple sequences
- MSA editor windows, one for each input file
You can override the defaults and require either that all sequences are opened in individual windows, or that all sequences are opened in a single MSA editor window.
In the File | Open dialog box, the Open Multiple Sequence Files As drop-down menu allows you to make this choice.
When Multiple Alignment is chosen, all sequences are opened in a single MSA editor window. If the sequences are unaligned and are of unequal length, gap symbols are appended to the end of the shorter sequences to make the lengths equal. When Single Sequences are chosen, all sequences are opened in individual sequence windows. You can also merge existing alignments
1. Choose File | Open. The Open File dialog box is displayed.
2. Select the sequence files you want to open.
3. Select the Open Multiple Sequences As arrow button and choose an option from the drop-down menu:
- Auto: MacVector will use the default guidelines to open the files
- Multiple Alignment: All sequences will be opened in a single MSA editor window
- Single Sequences: All sequences will be opened in individual sequence windows.
4. Select Open to open the sequence files.
You can create an empty MSA document in MacVector. This is particularly useful if you want to import aligned sequences from databases or Web pages, by cutting and pasting from other applications. You may also want to type sequences into an empty MSA document.
- From the File menu, choose either New Nucleic Acid Alignment orNew Protein Alignment.
An MSA editor window of the appropriate type is displayed.
You can either type a sequence in the new window, or paste residues or full sequences from the clipboard. You can also add sequences from files.
- In the newly created window, the cursor will be in the top left-hand corner. Type the required sequence, using the spacebar to indicate any gaps. Depending on the state of the sequence type button, you can type in either DNA or RNA codes, but not both in the same window.
TIP: You can program the numeric keypad for entering sequences.
As you type the sequence, the sequence numbering will appear over the line at the set intervals.
- With the cursor in the top left corner of the MSAeditor window, choose Edit | Paste.
The clipboard contents will be inserted at the cursor position, as follows:
- If one or more full sequences have been selected for copying (see the "Adding and selecting sequences" help topic), they will be inserted as new sequences
- If, in a single sequence, only residues have been selected (i.e. not the sequence name), they will be pasted into the untitled sequence at the insertion point
- If the selection is a block extending over several sequences, it will be inserted as new sequences.
Adding and selecting sequences