Adding annotations
Annotations can be added to a sequence from the:
- Sequence view (
) (
) Select the region you want the annotation to cover, right-click on the selected region, and choose the option Add Annotation (
) from the menu.
Note that this also applies to other views displaying sequences such as sequence lists, alignments, etc.
For information about making selections that are not contiguous, see selecting parts of the sequence.
- Annotation Table view (
) Right-click anywhere in this view and select the option Add Annotation () from the menu. Note that this option is not enabled in sequence lists.
In both cases, a dialog opens where you can provide information about the annotation (figure 15.19).
Figure 15.19: The "Add Annotation" dialog.
The left-hand part of the dialog lists a number of Annotation types. When you have selected an annotation type, it appears in the Type field under "Properties" in the right-hand part of the dialog. Choosing an annotation type is mandatory. If you wish to use an annotation type that is not present in the list, simply enter the type manually in the Type field15.1.
The right-hand part of the dialog contains the following options:
- Name. The name of the annotation which can be shown on the label in the Sequence view (whether the name is actually shown depends on the preferences configured in the Annotation layout palette of the Side Panel).
- Type. Reflects the selection in the left-hand part of the dialog as described above. You can also choose a type directly from the drop-down list or manually enter your own annotation type.
- Region. If you have already made a selection, this field will show the positions of the selection. You can modify the region further using the "Advanced" option and the conventions of DDBJ, EMBL, and GenBank. The following are examples of how to use the syntax (based on these definitions):
- 467. Points to a single residue in the presented sequence.
- 340..565. Points to a continuous range of residues bounded by and including the starting and ending residues.
- <345..500. Indicates that the exact lower boundary point of a region is unknown. The location begins at some residue previous to the first residue specified (which is not necessarily contained in the presented sequence) and continues up to and including the ending residue.
- <1..888. The region starts before the first sequenced residue and continues up to and including residue 888.
- 1..>888. The region starts at the first sequenced residue and continues beyond residue 888.
- (102.110). Indicates that the exact location is unknown, but that it is one of the residues between residues 102 and 110, inclusive.
- 123^124. Points to a site between residues 123 and 124.
- join(12..78,134..202). Regions 12 to 78 and 134 to 202 should be joined to form one contiguous sequence.
- complement(34..126). Start at the residue complementary to 126 and finish at the residue complementary to residue 34 (the region is on the strand complementary to the presented strand).
- complement(join(2691..4571,4918..5163)). Joins regions 2691 to 4571 and 4918 to 5163, then complements the joined segments (the region is on the strand complementary to the presented strand).
- join(complement(4918..5163),complement(2691..4571)). Complements regions 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the region is on the strand complementary to the presented strand).
- Annotation notes. In this field, you can add more information about the annotations like comments and links. Click on the Add qualifier/key button to enter information. Select a qualifier which describes the kind of information you wish to add. If an appropriate qualifier is not present in the list, you can type your own qualifier. The pre-defined qualifiers are derived from the GenBank format. You can add as many qualifier/key lines as you wish by clicking the button. Redundant lines can be removed by clicking the delete icon (
). The information entered on these lines is shown in the annotation table and in the yellow box which appears when you hover the mouse cursor over the annotation. If you write a hyperlink in the Key text field, like e.g. "digitalinsights.qiagen.com", it will be recognized as a hyperlink. Clicking the link in the annotation table will open a web browser.
Click on OK to add the annotation.
Note! The annotation will be included if you export the sequence in GenBank, Swiss-Prot, or CLC format. When exporting in other formats, annotations are not preserved in the exported file.
Footnotes
- ... field15.1
- Note that your own annotation types will be converted to "unsure" when exporting in GenBank format. As long as you use the sequence in CLC format, your own annotation type will be preserved