The Multiple Sequence Alignment (MSA) editor is a tool for modifying and comparing the alignment of several selected sequences. It can be used to edit individual sequences in multiple alignments, and to delete parts of sequences and import other parts.
The MSA editor allows you to copy, move, insert, rename and delete sequences. You can also merge existing alignments. For your source material, you can select and use single or multiple sequences, or parts of sequences, from sequence windows, MSA editor windows, or other applications. The MSA editor incorporates familiar texteditor features, such as doubleclicking to select a "word"; (here, a contiguous sequence of residues) and moving by selecting and dragging.
The toolbar of the MSA Editor window contains a row of buttons that are used to perform special functions. From left to right, they are:
- Sequence type. For protein alignments, this button indicates proteins. For nucleic acid alignments, it indicates DNA or RNA. Clicking the button changes the interpretation of all the sequences between DNA and RNA.
- Lock. Click to toggle between closed and open positions. Sequences can only be altered when the padlock is open.
- Mode will change the displayed sequence, between DNA, translated DNA (AA) or DNA and AA. See the Translated DNA Alignments page for more information.
- Align: brings up the alignment dialog
- Phylogeny: Click this button to display the Phylogenetic Reconstruction dialog box. The button becomes enabled when the MSA editor window contains at least four sequences.
- Views. Click this button to display the Alignment Views dialog box.
- Prefs: Click this button to display the Multiple Alignment Options dialog box.
- Replica. Allows you to view multiple windows of the same sequence. Each window can be of a different view of the sequence.
- Blocking:. Drag the horizontal slider to set the number of residues in a block between 1 to 10.
- Dots: replaces all residues that match the consensus sequence with dots.
- Line Wrap:. Click to toggle between linear and page mode. In linear mode, each sequence is displayed on a single horizontal line, and sequences are aligned on top of each other. You use the horizontal scroll bar to scroll through the entire sequence. In page mode, the linear display is wrapped to fit into the window, as in a word processor. You use the vertical scroll bar to scroll through the sequence.
- Groups:. Click to display the Color Group Editor dialog box. This allows you to edit the colors and similarity groups used to calculate the consensus.
- Width: This slider controls the width of the displayed characters in Color mode. Drag the slider to the left to reduce the width of the characters, and to the right to increase the width of the characters. If the character width is less than the width of the default font, the characters are represented as color bars only.
- Color: Click to toggle between the two display modes: color, and black and white. In black and white mode, sequences are displayed as monospaced black text on a white background. In color mode, sequences are displayed as black text with residue specific color backgrounds. To help visualize similarities during manual alignments, each amino acid or nucleotide can be assigned a unique color. Furthermore, groups of amino acids can be given colors to permit visual alignments based on properties. The color groups can be edited using the Color Group Editor dialog box.
POSITION MASK
A positionmasking bar can be displayed across the top of the aligned sequences. It is used in phylogenetic analysis, to exclude positions in the sequence from the analyses. For instructions, refer to the Position masking help topic.
Related Topics.
Aligning translated DNA sequences.
Picture tab
Domain coloring
Setting MSA Editor display options
Calculating a consensus line
Displaying a consensus line
Working with color groups
Remove gaps
