Introduction
IGB 6.5 introduces a new feature: the Sequence Viewer.
Starting with IGB 6.5, users have the option to view a region of sequence in a new Sequence Viewer window that displays sequence in two different modes: cDNA (spliced) or genomic.
When you right-click an item in the display, such as a gene model, you'll see a menu offering a new option: View Genomic Sequence in Sequence Viewer.
Also, if you've loaded a segment of genomic sequence, you click-drag a region of it to select it. If you right-click a region of selected sequence, you'll see the same option.
View sequence for a gene model or other annotation
For gene models/ annotations, simply right click on the annotation and choose option View Genomic Sequence in Sequence Viewer.
Note: To choose a single exon (part of) a gene model, right-click the exon. To choose the entire gene model, right-click any of the introns or the label, if available.
Choosing View Genomic Sequence in Sequence Viewer opens the Sequence Viewer as shown below.
By default, the Viewer depicts exonic bases in yellow and intronic bases in white against a black background. The start codon (ATG) is shown with a green box around it, and the stop codon has a red box around it.
Use the Colors menu to change the color scheme. For example, Blue on white depicts exons in blue and introns in black against a white background.
The title bar shows the name of the selected item.
For instance, the image below shows genomic sequence for gene model AT1G54330.1, from the A_thaliana_Jun_2009 genome version, on chromosome 1.
Show cDNA
After selecting a gene model, the Sequence Viewer allows you to select Show cDNA, which will eliminate introns from the displayed sequence. We recommend selecting this option before using the translation feature. If an individual exon is selected, this button will be available, but will not change the sequence.
After selecting this feature, you'll see just the exonic (block) sequence, and the button will read Show genomic.
Show translation
Translation options are accessed from the Show menu and include:
The + (forward) translations appears over the sequence; the - (reverse) translations below. The following image shows all 6 translations active.
Viewing Selected Sequence
IGB also allows you to directly select genomic DNA sequence to view. While this method loses the advantage of annotations/ exon designations, it does allow you to select DNA from introns, upstream and downstream regions, or any other area which may contain sequence of interest (i.e. promoters, enhancer binding elements, etc.). The first step is to ensure the sequence is loaded (Data Access tab > Load All Sequence button OR > Load Sequence in View button). Select the sequence you wish to view by click-dragging the cursor over the sequence bar at any zoom level. A red outline will appear around the selected sequence. Note: This method of genomic DNA selection also allows a direct copy to the clipboard, if you wish to skip the Sequence viewer. Simply right click within the selected sequence, and chose Copy.
Right click within the selected area and chose View Genomic Sequence in Sequence Viewer. The sequence viewer will open as before, and the title will now show the genomic range of the sequence, the genome version, and the chromosome number. The Show cDNA option will be disabled, but all other options will remain. The DNA sequence will always be presented in the + (plus) direction. However, if your sequence of interest is the other strand, Show > Complement will provide the complement of the sequence (this is usable with all sequences).
The sequence viewer also allows you to save the reverse complement of the sequence you are viewing if you wish. Go to File > Save Reverse Complement.
Copying and Saving Sequence
As mentioned, you can copy selected sequence to the clipboard directly from the main window of IGB. Additionally, you can copy a selection or all of your sequence from the sequence viewer. Highlight the sequence of interest (as shown below) and use Edit > Copy selected sequence to clipboard. Then open a text editor of choice and paste the sequence.
You also have the option to save the sequence directly from the viewer into a fasta file. Fasta files can be shared and used for bioninformatics in this file format, but fasta files can also be opened and viewed from any text editor to access the sequence directly. The file will contain the sequence as well as a line with all of the relevant information from the title of the sequence viewer window. We allow you to save the sequence directly or in the reverse complement, as you need. Open File > Save as Fasta or Save as Fasta (reverse complement).