Groups
Alignments can be grouped together so that they can be sorted/highlighted/hidden etc.
Creating a group from a selection:
- Select the sequences you wish to include in the group by left-clicking their rows in the detail view. Multiple rows can be selected by holding the Ctrl or Shift keys while clicking.
- Right-click and select 'Create Group', or use the Shift-Ctrl-G shortcut key. (Note that Ctrl-G will also shortcut to here if no groups currently exist.)
- Ensure that the 'From selection' radio button is selected, and click 'OK'.
Creating a group from a sequence name:
- Right-click and select 'Create Group', or use the Shift-Ctrl-G shortcut key. (Or Ctrl-G if no groups currently exist.)
- Select the 'From name' radio button and enter the name of the sequence in the box below. You may use the following wildcards to search for sequences: '*' for any number of characters; '?' for a single character. For example, searching for '*X' will find all sequences whose name ends in 'X' (i.e. all exons).
- Click 'OK'.
Creating a group from sequence name(s):
- Right-click and select 'Create Group', or use the Shift-Ctrl-G shortcut key. (Or Ctrl-G if no groups currently exist.)
- Select the 'From name(s)' radio button.
- Enter the sequence name(s) in the text box.
- You may use the following wildcards in a sequence name: '*' for any number of characters; '?' for a single character. (For example, searching for '*X' will find all sequences whose name ends in 'X', i.e. all exons).
- You may search for multiple sequence names by separating them with the following delimiters: newline, comma or semi-colon.
- You may paste sequence names directly from ZMap: click on the feature in ZMap and then middle-click in the text box on the Groups dialog. Grouping in Blixem works on the sequence name alone, so the feature coords will be ignored.
- Click 'OK'.
Creating a temporary 'match-set' group from the current selection:
- You can quickly create a group from a current selection (e.g. selected features in ZMap) using the 'Toggle match set' option.
- To create a match-set group, select the required items (e.g. in ZMap) and then select 'Toggle match set' from the right-click menu in Blixem, or hit the 'g' shortcut key.
- To clear the match-set group, choose the 'Toggle match set' option again, or hit the 'g' shortcut key again.
- While it exists, the match-set group can be edited like any other group, via the 'Edit Groups' dialog.
- If you delete the match-set group from the 'Edit Groups' dialog, all settings (e.g. highlight color) will be lost. To maintain these settings, clear the group using the 'Toggle match set' menu option (or 'g' shortcut key) instead.
Editing groups:
To edit a group, right-click and select 'Edit Groups', or use the Ctrl-G shortcut key. You can change the following properties for a group:
- Name: you can specify a more meaningful name to help identify the group.
- Hide: tick this box to hide the alignments in the alignment lists.
- Highlight: tick this box to highlight the alignments.
- Color: the color the group will be highlighted in, if 'Highlight' is enabled. The default color for all groups is red, so you may wish to change this if you want different groups to be highlighted in different colors.
- Order: when sorting by Group, alignments in a group with a lower order number will appear before those with a higher order number (or vice versa if sort order is inverted). Alignments in a group will appear before alignments that are not in a group.
- To delete a single group, click on the 'Delete' button next to the group you wish to delete.
- To delete all groups, click on the 'Delete all groups' button.
Settings
The settings menu can be accessed by right-clicking and selecting Settings, or by the shortcut Ctrl-S. Soome settings (those in the 'Features' and 'Display options' panes on the dialog, as well as the column widths) are saved to the file ".blixemrc" in your home directory when you quit Blixem, and will be restored the next time Blixem is run. To revert to the default settings, just delete the ".blixemrc" file.
- Highlight variations:Tick this box to highlight bases in the reference sequence that have SNPs, insertions, deletions etc. Hover over a highlighted base to see details of the variation in the feedback area.
- Show variations track:The variations track shows the details of the variations. Double-click on a variation to open its URL. The Highlight-Variations option must be enabled to use this option. A shortcut to quickly enable both options is to double-click the reference sequence. Double click the reference sequence again to hide the variations track.
- PolyA tails:Tick this option to show polyA tails in the alignment lists. By default polyA tails are only shown for the currently-selected sequence(s). To show them for all sequences, un-tick the 'Selected sequences only' box. When a polA tail is displayed, polyA signals are also highlighted in the reference sequence.
- Show Unaligned Sequence:Show any additional unaligned parts of the match sequence at the start/end of the alignment. Specify the number of additional bases to show in 'Limit to... bases', or untick this option to show all of the unaligned sequence. Tick the 'Selected sequences only' option to only show unaligned sequence for the currently selected sequence(s). Note that this option does not work with the 'Squash Matches' option, so it will not do anything if 'Squash Matches' is on.
- Show Splice Sites:Shows splice sites for the currently-selected alignment(s). Splice sites are highlighted on the reference sequence in green (for canonical) or red (for non-canonical). Blixem identifies GT-AG, GC-AG and AT-AC introns as canonical.
- Highlight Differences:When this option is set, matching bases are blanked out and mismatches are highlighted, making it easier to see where alignments differ from the reference sequence.
- Squash Matches:Group multiple alignments from the same sequence together into the same row in the detail view, rather than showing them on separate rows.
- Columns:Show/hide columns or edit the width of columns (in pixels). Click the 'Load optional data' button to load the data for the optional columns such as organism and tissue-type - then tick the check box to show this column in the Blixem window. The optional columns are greyed out if their data is not loaded. Once optional data is loaded you can also sort by it. Note that optional data is loaded on startup for DNA matches but not for protein matches, because the latter can be slow. The Load Optional Data button will be greyed out if optional data is already loaded.
- Grid properties:Set the maximum/minimum %ID values shown in the big picture. Expand or contract the grid scale by adjusting '%ID per cell'. The ID per cell can be set to as low as 0.1. Note that setting a low ID-per-cell can result in a large number of cells and hence a very large grid, and Blixem is not currently very clever about dealing with this.