Hello and welcome to IGB 6.5!
The following new features debuted in IGB 6.5, released in April 2011.
Most of these new features come from you - the IGB user and developer community.
As always, the IGB team relies on you, the user, to suggest ways we can improve the IGB software. Please keep sharing your ideas!
Sequence Viewer
For the release of IGB 6.5, we have created a Sequence Viewer. When you right-click an item in the main IGB data display, you'll see a new option offering to display genomic sequence. Choosing this option opens the Sequence Viewer, shown below.
The Sequence Viewer can display all six frames of translation (Show menu), a spliced cDNA (Show cDNA button), or change the color scheme. Exons and introns in gene models appear as different colors, and the viewer also marks start and stop codons, if available. You also have the option to view complementary strand sequence. You can copy and paste sequence or save it to a file using the File menu.
IGB 6.5 also makes it easier to work with genomic sequence bases. Just load the sequence in the usual way and then click-drag across the sequence of interest to select it. Right-click to open the Sequence Viewer or just press Control-C to copy.
For more information, read Genome sequence viewer.
Tabbed Panels and Tray Layouts
To give you greater flexibility in setting up your personal IGB environment, we have made some changes in the main IGB window. Upon start up, you will now see panels on the right as well as the bottom of the main window. These panels (also called trays) contain all of the usual tabs. The main difference is that you can move them out of the way by clicking the active tab, freeing more space for data exploration.
As always, clicking any tab will open it in the usual way. As with previous versions, you can open tabs in a new window. Now, however, you can move them to left, right, or bottom trays, depending on the tab.
For more information, read Tabbed panels.
More Zooming and Panning Options
IGB 6.5 introduces several new ways to pan (scroll) and zoom.
IGB now includes two tool buttons, Select and Grab, next to the horizontal zoomer. Click the 'hand' button (outlined in red below) to choose the Grab tool. Then click and drag the tool on the display to move left or right, and up or down. To select items, choose the Select tool (arrow cursor).
A new zoom feature allows you to "jump zoom" to a region by click-dragging (using the Select tool) over the central axis - the number line in the center of the display. Just click-drag over the region of interest, and release. IGB will jump and zoom to the highlighted region.
For more information, read Panning the Display or Zooming.
Autoload for BAM files
A new optional Autoload Mode (for BAM files) tells IGB to automatically load data from a file or URL once you've zoomed in far enough. A marker appears above the horizontal zoomer indicating the zoom level that triggers automatic loading of data.
Visualize insertions and deletions
Another feature is that IGB can now show both insertions and deletions in short reads. Insertions appear as a pair of red residues, indicating the point of insertion. Details about the insertion can be gotten from the Selection Info panel or by hovering the mouse over the red residues to activate the tooltip; this information contains the length and sequence of the insertion. Deletions appear as a 'dash', highlighted by default as gray; by opening File > Preferences > Other Options, you can set the 'other nucleotides' to appear as any color you like. This will highlight the deletions, as well as unloaded sequence, or 'N' reads in your selected color.
Create a mismatch graph
IGB now provides the opportunity to create a mismatch graph from BAM files. This bar graph shows how many mismatched reads are present at each nucleotide. You simply select the the track, right click in the label and open the menu; you are now offered the option of Make Mismatch Graph, along with the regular option of Make Annotation Depth Graph. By hovering over a position in the mismatch graph, a tooltip with information about nucleotide distribution will appear. This allows a user to quickly and easily find out how many mismatched nucleotides in total, as well as how many of which type, are represented in the reads at any single genomic location. This can be very useful in SNP identification and allelic determination. For more information on making either graph type, read Creating graph tracks from annotations tracks.
Plug-Ins
We have instituted the ability for IGB to accept plug-ins, allowing developers and users to create small 'add in' programs that customize the functionality of IGB. Each plug-in can perform a function or series of functions for a specific purpose. By selecting the right plug-ins to add, the user expands the usefulness of IGB and tailors it to their needs, without cluttering IGB with unnecessary functions. Some plug-ins, such as InverseTransformer and PowerTransformer are already available in the IGB program. These can be activated from the Plug-ins tab. The IGB developers will continue to author and make available some plug-ins; users can also write and use their own plug-ins, suited to their needs.
Expanded Support for Plant Genomics
IGB continues to allow access to publicly available DAS servers that support some plant genomes, but with version 6.5, the IGB team debuted a new IGB QuickLoad site with several sequenced plant or algal genomes not previously supported. We also moved the site to a faster server with improved internet connectivity, which should make your experience with IGB feel faster and more responsive.
To view the new IGB QuickLoad site, and see the full list of genomes we directly host, visit http://www.igbquickload.org/quickload.