The Commands menu is available by either pressing the Commands button at the top of the contig editor window, or by pressing the Control key and the left mouse button or by pressing right mouse button with the mouse cursor anywhere within the sequence display section of the contig editor. A menu will be revealed containing the following functions.
These options are described in greater detail below.
Performs a search. See section Searching.
Creates an annotation. See section Annotations.
Edits an annotation. See section Annotations.
Removes an annotation. See section Annotations.
This writes any edited data to disk. The undo history is cleared and it is no longer possible to quit and abandon these saved changes.
This outputs the current contig, as currently shown (e.g. with status lines) to a file. Ther user can select the region to dump and the file name to use.
This allows the user to employ the primer selection algorithm OSP to find primers for sequencing experiments. See section Primer Selection.
This performs a sequence alignment between the current selection on a reading and the consensus sequence. Pads are inserted in the consensus and/or readings as necessary. An application of this is easy extension of a reading: Simply highlight the extension required, select align, and adjust the cutoff marker.
One weakness of the alignment strategy used in the current shotgun assembly algorithm is that padding characters are not always aligned with one another. This function attempts to align padding characters using a very simply strategy. It does not solve all pad alignment problems but is a useful first step during cleaning-up operations.