Introduction
IGB tabbed panels provide an easy-to-use way access to multiple functions. Each panel contains information and/or functions involving loading data, exploring data, working with graphs, etc.
By clicking a tab, you can quickly review and explore available options and features without having to operate drop down menus for every function. The ability to open and hide these tabs at will also lets you optimize your use of available screen space.
The Tabbed Panels Overview
Data Access Panel
This panel provides an easy-to-use interface for loading data sets from diverse servers. The Data Access Panel displays hyperlinks to the Data Source Web sites that (typically) present more information about the organizations that created the data sets on offer in the IGB interface. If a data provider has associated URLs (Web pages) with individual data sets, IGB will display hyperlinked info buttons alongside the data set name. For more information, see Loading Data.
Selection Info Panel
This panel lists information about annotations/gene models/gene elements/ features selected in the display. This panel can also show meta-data about a selected track, i.e. the information about what server this data came from, a description of what it contains, and URLs for feature and servers. To use the Selection Info panel, click it. To find out detailed information about a track, click the track. To get more information about an item contained within a track, click it. A summary of this same information can be seen using the tool tips (hover the mouse over the annotation of interest). However information in the Selection Info panel can be highlighted and copied for use in other programs.
Search Panel
Use this panel to search for genes, alignments and sequences. Chose IDs or names, Residues or Properties. Clicking search results will tell IGB to scroll and zoom to that particular item. For ID or names, you can additionally search remote servers. In the bottom left of the Search panel, you will see the number of local and remote matches.
Sliced View Panel
This panel displays an alternative view of items selected in the main display. By making all of the introns an identical size of your choice (set in the Slice buffer box), you can see all of the exons at relative sizes to each other. The main, upper panel shows the genomic annotation; the lower panel shows the same gene in Sliced View, with the Slice buffer set at 10 (red box). The sliced view image concentrates on the exonic portions of the gene annotation. This view also allows ORF identification.
Graph Adjuster Panel
The Graph Adjuster panel has many features to help work with graph files, including the ability to change the type and color of the graphs. It also has many useful functions including combining graphs, mathematical transformations etc. For more details, see Working with graphs||\. This panel will also host new functions that affect graphs, which are introduced through Plug-ins. For more details, see Plug-ins.
External View Panel
The External View panel allows you to bring up all the data about a region that you are viewing from the UCSC server or ENSEMBL. To use ENSEMBL you must have a fairly zoomed in picture (>100,000bp) and it must be a species that ENSEMBL curates. The same is true for UCSC, although it can handle slightly larger regions of the chromosome. A smaller region or specific gene may return more data due to more details being available. You can NOT interact with this view, but you can get interesting details about a gene/region. The information that is brought can include mapped ESTs, SNPs, cross species comparisons, repeated sequence data, as well as basic gene annotations. As a caution, the larger the region in the inquiry, the slower it will be to load the information. Every time you move to a new area, you will need to click the update button.
Plug-ins Panel
A new panel introduced in IGB 6.5, this panel allows you to manage your Plug-ins. You can browse plug-in repositories, add in plug-ins that are useful or remove out-dated ones. For more details, see Plug-Ins.
Current Sequence Panel
In IGB 6.5, this sub-panel of Data Access was moved into an independent tab. The Current Genome panel appears on the right side (can be moved to the left side) and allows you to navigate through the loaded sequences, which are usually either chromosomes or contigs. The list of sequences can be sorted by sequence name or by size; click the label for the appropriate column to change the sorting.
Restriction Sites Panel
This panel allows you to map restriction sites to your sequence. Select the enzyme(s) of interest from the list, using control/command to select additional enzymes; notice that each enzyme is assigned a separate color. Click the Map Sites button, and bars of matching color will show where each restriction site occurs within the sequence. You can click-zoom to a particular hash mark to see the sequence in question. The Clear button will allow you to start over with different enzymes if you chose.
Bookmarks Panel
The Bookmarks tab starts hidden, but can be opened from View > Tabs > Bookmarks, in which you can check the tray location you would like to have it opened in. This panel allows you to manage and list all of the IGB bookmarks you have. For more details about Bookmarks, see Bookmarks||\.