GENtle/Alignments

Alignment.

The alignment module displays alignments of DNA and amino acid sequences. It can be invoked through Tools/Alignment or Ctrl-G.

Settings dialog

The settings dialog will be invoked upon starting the module, or through the "settings" button in the toolbar. The sequences to align, their order, and the alignment algorithm and its parameters can be chosen here. The following algorithms are available:

Clustal-W	This (default) algorithm generates alignments of high quality, but is rather slow for simple alignments, and sometimes stumbles over local alignments.
Smith-Waterman	An internal, fast, but simple algorithm for local alignments, that is, aligning one or multiple short sequences againast a long one. The long sequence has to be the first. It works great for checking sequencing data against the expected sequence.
Needlemann-Wunsch	An internal, fast, but simple algorithm for global alignments, that is, aligning sequences of roughly the same length (e.g., different alleles of a gene). As with Smith-Waterman, all alignments are made against the first sequence.

Caveat : Clicking OK in this dialog will recalculate the alignment; the previous alignment and all manual changes made to it will be lost.

Toolbar

Several functions and display options can be invoked in the tool bar:

• Enter sequence
• Open sequence
• Save sequence
• Print sequence
• Settings
• Horizontal mode
• Middle mouse button function

View menu

Some display options can be combined with each other:

• Bold (shows characters in bold)
• Mono (black-and-white mode)
• Conserved (shows characters that match the one in the first line as dots)
• Identity (toggles the "identity" line)

Some of them exclude one another:

• Normal (shows colored text on white background)
• Inverted (shows white text on colored background)

Some other display options are planned, but not implemented as of now.

Sequence display

The sequence map can be altered through the context menu. These changes will only alter the display, not recalculate the alignment.

• Lines can be moved up or down
• Features for each line can be shown or hidden. By default, features for the first line are shown, features of the other lines are hidden.
• Gaps can be inserted or deleted, in this line, or all except this line. One of these four possible functions is additionally assigned to the middle mouse button; this setting can be changed in the toolbar.
• A double click on a character (not on a gap) opens the "source" window for that sequence (if available), marks and shows the position that was clicked in the alignment. This can be helpful for checking a sequencing.
• Sequences can be marked across multiple lines, then formatted via the Appearance context menu.

Sequences can not be edited within the alignment module. For that, you will have to edit the original sequence, then re-run the alignment.

Notes

• Legend for the ClustalW consensus line:

* = identical or conserved residues in all sequences in the alignment

: = indicates conserved substitutions

. = indicates semi-conserved substitutions