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 is also bound to the Control-x Control-s key sequence.
This outputs the current contig, as currently shown (e.g. with status lines) to a file. The user can select the region to dump, the length of each line, and the file name to use.
This command produces a trace file for the consensus sequence by averaging the traces of the readings used to produce this trace. The command brings up a dialogue containing controls to specify the filename, the consensus start and end positions, the strand, and whether to use matching reads.
As the trace of a reading is dependent on the direction it was read, the consensus trace can be computed from all the reads in either the forward or reverse directions, but not both at once. When the "Use only matching reads" toggle is set to "Yes" only the readings of the correct strand that have the same base call as the consensus sequence are used. This is useful for producing wild-type trace files for a mutation analysis project.
This operates in a very similar manner to the main Gap4 List Confidence command (see section List Confidence), except that it only operates on the one contig (that being displayed in the editor) and it uses the current editor consensus confidences rather than the ones saved to disk. It displays a dialogue requesting a range within the contig and a question asking whether only the summary is required.
Pressing OK or Apply will add to the editor information line a count of the expected number of errors and the error rate. If the "Only update information line" question was answered as No then the full frequency table will also be output t the main text output window in the same format as the List Confidence command in the main Gap4 View menu. The Apply button can be used to calculate the number of errors without destroying the dialogue. This can be useful where the option is needed on a frequent basis.
It is sometimes useful to try selecting a range from the dialogue that includes all of the contig except for around 1000 bases from each end. Experience has shown that it is often the very ends of contigs (which are generally low coverage and bad quality) that have most of the errors.
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 readings as necessary. It provides a simple way of extending the visible part of a reading to use its hidden data. 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. Additionally, after shuffling, all columns consisting entirely of pads will be removed.
Marks a reading for subsequent removal. See section Removing Readings
Breaks the contig into two with the reading underneath the editing cursor as the left end of the new contig. In order to perform this operation all edits are saved automatically first. Once saved these edits cannot be undone. This operation is identical to the Break Contig command in the main menu.See section Break Contig.