Introduction
IGB loads and displays sequence data, alone or in conjunction with other files. Genomic sequence data always appears in its own track underneath the number line, which represents genomic sequence base coordinates. IGB supports copying and pasting sequence from IGB into other programs, as well as opening a separate viewer to explore sequence data.
Because sequence data can be quite large, IGB makes it easy for you to load just part of the sequence data, or all the sequence available for the current chromosome, using controls in the Data Access panel.
Loading Sequence Data
Loading the Reference Sequence
To load the publicly available reference sequence (refseq) for the current chromosome, click Load All Sequence button in the Data Access panel.
However, some genomes are enormous and loading the entire genome's worth of sequence into IGB is not necessary, and impractical. IGB makes it easy for you to perform partial loading of sequence; zoom to a region of interest, and click the Load Sequence in View button in the Data Access panel. If the genome you're viewing has a partial sequence data server associated with it, then the sequence data will load. If not, you will see an error message that there is currently no partial sequence server for your genome. If this happens, you can click Load All Sequence, which will attempt to locate a file with whole chromosome sequence available for your genome.
Tip: If you are working with a genome that doesn't have a partial sequence server, please contact us! We may be able to add it quite easily to the BioViz DAS2 data source, which supplies partial genome sequence for many genomes, including some not supported by UCSC Genome Bioinformatics, Ensembl, or other major data providers.
Warning: Some partial sequence data servers will reject requests for residues from a region that is too large. Others will return the data, but only after a very long wait. BioViz DAS2, or any other DAS2 server for that matter, will send you the data very quickly. Ensembl and UCSC DAS servers tend to be slow, but they seem to respond eventually. If you notice any problems, open the Console window (Help > Show Console) and take a look at any error messages you may see. And please let us know so that we can improve IGB and make it more robust
Other sequences as a reference sequence
If you have a sequence file in one of the formats that IGB can read (File Formats), you can use that sequence as a reference sequence. Open the File menu and choose the option Open Reference Sequence.... You will need to select Species and Genome Version if they are not already selected. After IGB loads the file (it will appear in the Data Management table), you will need to use the Load Data button(s) to visualize the data in the main view.
Note: if the chromosome 'names' do not follow standard synonym conventions you may need to add synonyms (Personal Synonyms).
Note: If the actual sequence has a different length than the length of the annotation files, IGB will not be able to display them together. Please contact us through the forums if you need help with this issue.
Loading sequence as a track
If you want to load an additional sequence as a track rather than as a reference sequence (perhaps a substrain or an individual), IGB has several options. You can drag and drop the file into IGB from either a desktop folder or from a URL. Alternatively, you can File > Open File... or Open URL....A new place holder track will be made, and the file will appear in the Data Management table. Simply use the Load Data button(s) to visualize the sequence.
Viewing sequence
When the image is zoomed out as far as possible , such as showing the whole chromosome, loaded sequence will appear as a gray bar (default); the color can be changed from File > Preferences > Other Options 'other'. To view sequence data, zoom in until the letters become visible, using the horizontal slider or by double-clicking a smaller feature. The sequence is shown using the letters A, T, G and C to represent nucleotides and the letter N to represent positions where we don't know the identity of the base. The colors are set to default but can be changed in the Preferences > Other Options tab.
If the sequence is not loaded, then you'll see '-' characters in gray (default) when zoomed in. Note that depending on the sequence data server, file, or URL that supplied the sequence data, bases may appear in upper or lower case; IGB reads all sequence as case insensitive.
In the first image, you can see a sequence loaded as a track (red arrow). Notice that the refseq has not yet been loaded (blue arrow) since you see gray with '-' marks; zoomed out, you see a gray bar for the loaded track, and you see nothing in the coordinate axis for the reference sequence.
In the second image,you can see that the refseq is now loaded (red arrow). After the refseq is loaded, the sequence in the track (yellow arrow) changes to the FG color for that track (cyan in this case) where ever it matches the refseq. In this state, it will only highlight differences/mismatches with a letter and a color change. Zoomed out, the track appears as a solid bar in the FG color for the track. The refseq appears as a gray bar in the coordinate axis.
Copy and paste sequence bases in IGB
You can copy a sequence of bases and paste the sequence into another application, such as Notepad.
To capture a sequence of bases:
- Make sure that the sequence residues are already loaded.
- Either select a single annotation or click and drag in the Coordinates track to select the desired coordinate range.
- Choose Edit menu > Copy Selected Residues to Clipboard.
- Paste the text string into the target application or location.
Tip: If you have selected an annotation that has introns, the selected residues will only include the exon regions. This is a great way to get just the transcript sequence by itself, as derived from genomic!
Tip: If you have selected a negative-strand annotation, the selected residues will be reverse-complemented.
If you want to capture all the residues including the intron regions, select the region by dragging in the Coordinates track