alignment calculations, sequence display
Multiple Sequence Viewer/Editor —View Options Pane
Set display options for alignment calculations and sequence display.
To open this pane, click the View Options button in the Multiple Sequence Viewer/Editor Panel.
- Features
- Additional Resources
View Options Pane Features
- Alignment calculations section
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Select alignment properties and options for their calculation.
- Show options
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Select options to show the values from the alignment calculations in columns to the right of the sequences. The options are Identity %, Conservation %, Similarity %, Overall Score.
- Compute for columns buttons
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Compute the alignment properties for the chosen columns.
- All—compute for all columns in the reference sequence.
- Selected—compute for the columns that are selected in the reference sequence.
- Include gaps option
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Include gaps in the alignment property calculations.
- Sequence display section
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Set options for the display of sequences.
- Show properties link
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Add Maestro entry properties and descriptors to the display of sequence properties, or remove them from the display. Opens the Manage Sequence Properties dialog box. These properties are displayed to the right of the sequences. You can compute descriptors in the protein sequence descriptors, or the display results.
- Wrap sequences option
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Wrap the sequences so that the display consists of multiple rows of sequences, and can be scrolled vertically. When unselected, display the sequences in a single row that scrolls horizontally.
- Split Chain View option
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Display each chain on a separate line in the display area.
- Format buttons
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Click the button for the format to use for the residue text, either one-letter, three-letter, or no text.
- Identities buttons
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Click a button to apply the desired representation of identities: either the residue code or a dot. Using a dot makes it easy to find the mutations from the query sequence in the other sequences.
- Font Size buttons
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Click the − or + button to decrease or increase the font size for the residues.
Note: The chosen preferences for Wrap Sequences, Font Size, and Split Chain View options are automatically saved across sessions for both the MSV and the Workspace Sequence Viewer.